Rationale: This script performs differential gene expression (dge) and calculates the upregulated and downregulated genes in lichen samples versus Xanthoria culture samples using edgeR and Sleuth
counts<-read.delim2("../analysis_and_temp_files/06_meta_mapping/kallisto_mycobiont_only.txt",sep=" ")
metadata<-read.csv2("../analysis_and_temp_files/06_meta_mapping/metadata_shared_with_neha.csv",sep=",")
# Extract locus_tag from target_id (XANPAGTX0501 for nuclear genome and GTX0501mito for mito genome) - OPTIONAL
counts[c("locus_tag","rest")]<-str_split_fixed(counts$target_id,'_',n=2)
# Tabulate the counts
counts_tab<-pivot_wider(counts[c(1,4,6)],names_from=sample,values_from = est_counts)
head(counts_tab)
## # A tibble: 6 × 32
## target_id XBC2 XBA1 XSA2_2 XSC1 XSE2 XBE1 XTA2 XSC2 XSA2 XBA2 XBC1
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 XANPAGTX05… 270 535 593.5 248 335.5 288 484 324.5 429.5 408 324.5
## 2 XANPAGTX05… 194 131 284.5 112 171.5 132 257.5 144 179.5 187 81
## 3 XANPAGTX05… 191.5 305 264.5 152.5 288 367 332 246.5 187.5 140 367
## 4 XANPAGTX05… 126 43.5 119.5 60.5 40.5 34.5 87.5 45 73 258.5 43.5
## 5 XANPAGTX05… 38 223 221 91 38 20 267 98 179 196 32
## 6 XANPAGTX05… 205 431 487 176 180 86 332 271 320 356 114
## # ℹ 20 more variables: XTA1 <chr>, XSA1 <chr>, MP_I <chr>, XTC2 <chr>,
## # XTE2 <chr>, XBE2 <chr>, XMC2 <chr>, MP_II <chr>, S_21XB1 <chr>,
## # KS21XB1 <chr>, S_21XB3 <chr>, S_42XB1 <chr>, S_42XB2 <chr>, S_42XB3 <chr>,
## # KS48XB1 <chr>, KS48XB2 <chr>, KS48XB3 <chr>, KS9XB1 <chr>, KS9XB2 <chr>,
## # KS9XB3 <chr>
write.table(counts_tab,"../analysis_and_temp_files/08_dge_culture_lichen/counts_table.tsv",quote=F,sep="\t",row.names = F) # Final table that will be used for dge calculation
full<-read.delim("../analysis_and_temp_files/08_dge_culture_lichen/counts_table.tsv",row.names=1)
d<-full %>% select(-MP_I,-MP_II) #remove MP_I and MP_II samples (based on previous correlation heatmaps)
colnames(d)
## [1] "XBC2" "XBA1" "XSA2_2" "XSC1" "XSE2" "XBE1" "XTA2"
## [8] "XSC2" "XSA2" "XBA2" "XBC1" "XTA1" "XSA1" "XTC2"
## [15] "XTE2" "XBE2" "XMC2" "S_21XB1" "KS21XB1" "S_21XB3" "S_42XB1"
## [22] "S_42XB2" "S_42XB3" "KS48XB1" "KS48XB2" "KS48XB3" "KS9XB1" "KS9XB2"
## [29] "KS9XB3"
head(d,5:5)
## XBC2 XBA1 XSA2_2 XSC1 XSE2 XBE1 XTA2 XSC2 XSA2
## XANPAGTX0501_000001-T1 270.0 535.0 593.5 248.0 335.5 288.0 484.0 324.5 429.5
## XANPAGTX0501_000002-T1 194.0 131.0 284.5 112.0 171.5 132.0 257.5 144.0 179.5
## XANPAGTX0501_000003-T1 191.5 305.0 264.5 152.5 288.0 367.0 332.0 246.5 187.5
## XANPAGTX0501_000004-T1 126.0 43.5 119.5 60.5 40.5 34.5 87.5 45.0 73.0
## XANPAGTX0501_000005-T1 38.0 223.0 221.0 91.0 38.0 20.0 267.0 98.0 179.0
## XBA2 XBC1 XTA1 XSA1 XTC2 XTE2 XBE2 XMC2 S_21XB1
## XANPAGTX0501_000001-T1 408.0 324.5 467.5 262 364.5 292.5 164.5 353.0 700.0
## XANPAGTX0501_000002-T1 187.0 81.0 178.5 163 199.0 183.0 99.0 113.0 66.5
## XANPAGTX0501_000003-T1 140.0 367.0 414.5 134 366.5 319.0 164.5 364.5 151.5
## XANPAGTX0501_000004-T1 258.5 43.5 59.5 74 53.0 29.5 47.0 27.5 11.0
## XANPAGTX0501_000005-T1 196.0 32.0 390.0 196 122.0 100.0 13.0 41.0 22.0
## KS21XB1 S_21XB3 S_42XB1 S_42XB2 S_42XB3 KS48XB1 KS48XB2
## XANPAGTX0501_000001-T1 302.5 716.0 452.5 333.0 356.5 454.5 462.5
## XANPAGTX0501_000002-T1 121.5 48.5 126.5 67.0 73.0 221.0 176.5
## XANPAGTX0501_000003-T1 216.0 142.0 206.5 202.5 217.5 197.5 214.0
## XANPAGTX0501_000004-T1 212.0 43.5 68.5 97.5 79.5 43.5 45.5
## XANPAGTX0501_000005-T1 17.0 22.0 27.0 19.0 56.0 16.0 17.0
## KS48XB3 KS9XB1 KS9XB2 KS9XB3
## XANPAGTX0501_000001-T1 464.0 376.0 297.0 323.5
## XANPAGTX0501_000002-T1 236.5 98.0 90.0 106.0
## XANPAGTX0501_000003-T1 209.0 313.5 216.5 268.5
## XANPAGTX0501_000004-T1 37.5 91.5 36.0 78.5
## XANPAGTX0501_000005-T1 6.0 24.0 21.0 21.0
# create new column, "max" for the max read count in each row
d$max<-apply(d,1,max)
min(d$max)
## [1] 0
d1<-d[which(d$max>=5),] #to remove lowly expressed genes, keep rows in which max read count across whole panel is atleast 5
# drop the max column, as its not needed anymore
raw_counts<-d1 %>% select(-max)
length(rownames(d1)) # total number of genes
## [1] 11105
length(rownames(raw_counts)) # number after removal of lowly expressed genes
## [1] 11105
library(sleuth)
kal_dirs <- data.frame("sample"=metadata$run_id, "condition"=metadata$sample_type,
"path"=paste0("../analysis_and_temp_files/06_meta_mapping/kallisto_meta_mapping/",metadata$run_id,"_kallisto")) %>% filter(sample!="MP_II" & sample!="MP_I")
#define list of genes to be included: only mycobiont and only those that have read count across whole panel of >=5
target_id<-rownames(d1)
so <- sleuth_prep(kal_dirs, extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## .............................
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11105 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## .............................
so <- sleuth_fit(so, ~condition, 'full')
## fitting measurement error models
## shrinkage estimation
## 16 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000408-T1, XANPAGTX0501_000967-T1, XANPAGTX0501_000968-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_000995-T1, XANPAGTX0501_002621-T1, XANPAGTX0501_002938-T1, XANPAGTX0501_004237-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_008798-T1, XANPAGTX0501_009179-T1, XANPAGTX0501_010285-T1, XANPAGTX0501_010514-T1, XANPAGTX0501_010642-T1, XANPAGTX0501_010694-T1
## computing variance of betas
so <- sleuth_fit(so, ~1, 'reduced')
## fitting measurement error models
## shrinkage estimation
## 16 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000408-T1, XANPAGTX0501_000967-T1, XANPAGTX0501_000968-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_000995-T1, XANPAGTX0501_002621-T1, XANPAGTX0501_002938-T1, XANPAGTX0501_004237-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_008798-T1, XANPAGTX0501_009179-T1, XANPAGTX0501_010285-T1, XANPAGTX0501_010514-T1, XANPAGTX0501_010642-T1, XANPAGTX0501_010694-T1
## computing variance of betas
so <- sleuth_lrt(so, 'reduced', 'full')
so <- sleuth_wt(so, 'conditionxanthoria_culture')
plot_pca(so, color_by = 'condition', text_labels = TRUE,use_filtered=T,units="tpm")
sleuth_table <- sleuth_results(so, 'conditionxanthoria_culture')
sig <- sleuth_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "culture", ifelse(b< -1, "lichen", "low_logFC")))
table(sig$change)
##
## culture lichen low_logFC
## 564 1185 4124
pca<-plot_pca(so, color_by = 'condition', text_labels = F,use_filtered=T,units="tpm")
pca+theme_bw()+theme(text=element_text(size=7))
ggsave('../results/lichen_culture_pca.pdf',width = 4.5, height = 3)
plot_pc_variance(so,use_filtered=T,units="tpm")
ppv <- plot_pc_variance(so,use_filtered=T,units="tpm")
PCpc <- ppv$data$var
names(PCpc) <- paste0("PC", seq(1:length(PCpc)))
PCpc
## PC1 PC2 PC3 PC4 PC5
## 58.442702 23.237991 6.167265 3.743065 2.602711
funannot<-read.delim2("../../02_mycobiont_genome/analysis_and_temp_files/06_annotate_lecanoro/Annotation_with_OG.txt",sep="\t")
sig2<-sig %>% left_join(funannot, by=c("target_id"="TranscriptID"))
upreg_sl=sig2 %>% filter(change=="lichen") %>% select(-c(CDS.transcript,Translation,gDNA,mRNA))
downreg_sl=sig2 %>% filter(change=="culture")%>% select(-c(CDS.transcript,Translation,gDNA,mRNA))
write.table(upreg_sl, "../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_lichen_sleuth.txt", append="false", sep = "\t", quote=F, row.names = F)
write.table(downreg_sl, "../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_culture_sleuth.txt", append="false", sep = "\t", quote=F, row.names = F)
tabd_df <- so$obs_norm[so$obs_norm$target_id %in% target_id,]
tabd_df <- dplyr::select(tabd_df, target_id, sample,
tpm)
tabd_df <- reshape2::dcast(tabd_df, target_id ~ sample,
value.var = "tpm")
write.table(tabd_df, "../analysis_and_temp_files/08_dge_culture_lichen/norm_counts_sleuth.txt", append="false", sep = "\t", quote=F, row.names = F)
plot_bootstrap(so,
target_id = sig$target_id[which.max(sig$b)],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = sig$target_id[which.min(sig$b)],
units = "est_counts",
color_by = "condition")
sig$b[which.min(abs(sig$b))] and the q-value (p-value adjusted for multiple test correction) is sig$qval[which.min(abs(sig$b))], but you can see the difference between sample types somewhatplot_bootstrap(so,
target_id = sig$target_id[which.min(abs(sig$b))],
units = "est_counts",
color_by = "condition")
###make table with GO annotations
go_df <-funannot %>% select(TranscriptID,GO.Terms_new) %>%
mutate(GO.Terms_new = strsplit(GO.Terms_new, ",")) %>%
unnest(GO.Terms_new) %>%
mutate(GO.Terms=sub(".*? ", "", GO.Terms_new),
short_term = substr(GO.Terms, 1,40))
go_data <- list(
term2protein = data.frame(
term = go_df$GO.Terms_new,
gene = go_df$TranscriptID
),
term2name = data.frame(
term = go_df$GO.Terms_new,
name = go_df$short_term
),
universe = unique(as.character(go_df$TranscriptID))
)
### select genes upregulated in lichens and order them by fold change
geneList5 = sig$b[sig$change=="lichen"]
names(geneList5) = sig$target_id[sig$change=="lichen"]
geneList5 = sort(geneList5, decreasing = F)
geneList5 <- names(geneList5)
###enrichment analysis
enrich5<-clusterProfiler::enricher(geneList5,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=go_data$universe,
TERM2GENE=go_data$term2protein,
TERM2NAME=go_data$term2name)
##
## Registered S3 methods overwritten by 'treeio':
## method from
## MRCA.phylo tidytree
## MRCA.treedata tidytree
## Nnode.treedata tidytree
## Ntip.treedata tidytree
## ancestor.phylo tidytree
## ancestor.treedata tidytree
## child.phylo tidytree
## child.treedata tidytree
## full_join.phylo tidytree
## full_join.treedata tidytree
## groupClade.phylo tidytree
## groupClade.treedata tidytree
## groupOTU.phylo tidytree
## groupOTU.treedata tidytree
## is.rooted.treedata tidytree
## nodeid.phylo tidytree
## nodeid.treedata tidytree
## nodelab.phylo tidytree
## nodelab.treedata tidytree
## offspring.phylo tidytree
## offspring.treedata tidytree
## parent.phylo tidytree
## parent.treedata tidytree
## root.treedata tidytree
## rootnode.phylo tidytree
## sibling.phylo tidytree
## Registered S3 method overwritten by 'ggtree':
## method from
## identify.gg ggfun
enrichplot::dotplot(enrich5,showCategory=40,label_format=40)
enrich5_pairwise<-enrichplot::pairwise_termsim(enrich5)
enrichplot::emapplot(enrich5_pairwise)
### select genes upregulated in lichens and order them by fold change
geneList6 = sig$b[sig$change=="culture"]
names(geneList6) = sig$target_id[sig$change=="culture"]
geneList6 = sort(geneList6, decreasing = T)
geneList6 <- names(geneList6)
###enrichment analysis
enrich6<-clusterProfiler::enricher(geneList6,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=go_data$universe,
TERM2GENE=go_data$term2protein,
TERM2NAME=go_data$term2name)
enrichplot::dotplot(enrich6,showCategory=40,label_format=40)
enrich6_pairwise<-enrichplot::pairwise_termsim(enrich6)
enrichplot::emapplot(enrich6_pairwise)
###make table with IPS annotations
ips_df <-funannot %>% select(TranscriptID,InterPro_new) %>%
mutate(InterPro_new = strsplit(InterPro_new, ", I")) %>%
unnest(InterPro_new) %>% mutate(InterPro_new=str_replace(InterPro_new,"^PR","IPR")) %>%
mutate(short_term = substr(InterPro_new, 1,40))
ips_data <- list(
term2protein = data.frame(
term = ips_df$InterPro_new,
gene = ips_df$TranscriptID
),
term2name = data.frame(
term = ips_df$InterPro_new,
name = ips_df$short_term
),
universe = unique(as.character(ips_df$TranscriptID))
)
enrich7<-clusterProfiler::enricher(geneList5,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrichplot::dotplot(enrich7,showCategory=40,label_format=40)
* Upregulated in lichen as a graph
enrich7_pairwise<-enrichplot::pairwise_termsim(enrich7)
enrichplot::emapplot(enrich7_pairwise)
pdf(file="../results/lichen_upr.pdf",width=5,height=4)
enrichplot::emapplot(enrich7_pairwise,cex_label_category=0.4,cex_line=0.25,
shadowtext=F,cex_pie2axis=0.1,repel=T)
dev.off()
## quartz_off_screen
## 2
enrich8<-clusterProfiler::enricher(geneList6,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrichplot::dotplot(enrich8,showCategory=40,label_format=40)
* Upregulated in culture as a graph
enrich8_pairwise<-enrichplot::pairwise_termsim(enrich8)
enrichplot::emapplot(enrich8_pairwise)
pdf(file="../results/culture_upr.pdf",width=5,height=4)
enrichplot::emapplot(enrich8_pairwise,cex_label_category=0.4,cex_line=0.25,
shadowtext=F,cex_pie2axis=0.1,repel=T)
dev.off()
## quartz_off_screen
## 2
perc<-funannot %>% mutate(go_annotated=ifelse(!(is.na(GO.Terms_new)),"Annotated","Non-annotated"),
ipr_annotated=ifelse(!(is.na(InterPro_new)),"Annotated","Non-annotated"),
gene_set=case_when(
TranscriptID %in% sig$target_id[sig$change=="culture"] ~ "Upregulated in culture",
TranscriptID %in% sig$target_id[sig$change=="lichen"] ~ "Upregulated in lichen",
T ~ "non-DGE"))
ipr_perc_dge<- perc %>% group_by(gene_set,ipr_annotated) %>% summarize(n=n()) %>% mutate(database="InterPro",annotated=ipr_annotated) %>% select(-ipr_annotated)
## `summarise()` has grouped output by 'gene_set'. You can override using the
## `.groups` argument.
go_perc_dge <- perc %>% group_by(gene_set,go_annotated) %>% summarize(n=n()) %>% mutate(database="GO",annotated=go_annotated) %>% select(-go_annotated)
## `summarise()` has grouped output by 'gene_set'. You can override using the
## `.groups` argument.
ipr_perc_all<- perc %>% group_by(ipr_annotated) %>% summarize(n=n()) %>% mutate(database="InterPro",gene_set="Whole transcriptome",annotated=ipr_annotated) %>% select(-ipr_annotated)
go_perc_all <- perc %>% group_by(go_annotated) %>% summarize(n=n()) %>% mutate(database="GO",gene_set="Whole transcriptome",annotated=go_annotated) %>% select(-go_annotated)
perc2<-rbind(ipr_perc_dge,go_perc_dge,ipr_perc_all,go_perc_all)
perc2$annotated<-factor(perc2$annotated,levels=c("Non-annotated","Annotated"))
ggplot(perc2 %>% filter(gene_set %in% c("Upregulated in culture","Upregulated in lichen")),
aes(x=database,y=n,fill=annotated))+geom_bar(position="stack",stat="identity")+
facet_wrap(~gene_set)
* Instead of two datatbases, visualize the number of proteins with any kind of functional annotation * NB: counted tRNA as being annotated
#make bar graph for DGE
perc<-funannot %>% mutate(annotated=ifelse(!(is.na(GO.Terms_new))| !(is.na(CAZyme_new))| !(is.na(PFAM_new))|
!(is.na(Protease_new))|!(is.na(InterPro_new))| KO!=""|Feature=="tRNA",
"Annotated","Non-annotated"),
gene_set=case_when(
TranscriptID %in% sig$target_id[sig$change=="culture"] ~ "Upregulated in culture",
TranscriptID %in% sig$target_id[sig$change=="lichen"] ~ "Upregulated in lichen",
T ~ "non-DGE"))
perc_dge<- perc %>% group_by(gene_set,annotated) %>% summarize(n=n()) %>%
group_by(gene_set) %>% mutate(perc=(100*n)/sum(n))
## `summarise()` has grouped output by 'gene_set'. You can override using the
## `.groups` argument.
dge_plot<-ggplot(perc_dge %>% filter(gene_set %in% c("Upregulated in culture","Upregulated in lichen")),
aes(x=gene_set,y=n,fill=annotated))+geom_bar(position="stack",stat="identity")+
geom_text(aes(label = paste0(round(perc,0),"%"),color=annotated), position=position_stack(vjust = 0.5),size=7)+
xlab("")+ylab("# of transcripts")+ggtitle("Differentially expressed")+
scale_fill_manual(values = c("Non-annotated"="#ffda73","Annotated"="#156902"))+
scale_color_manual(values = c("Non-annotated"="#156902","Annotated"="#ffda73"))+ theme_minimal()+
theme(legend.title=element_blank(),legend.position = c(0.2, 0.8),
legend.background = element_rect(fill="white",
linewidth=0.5, linetype="solid",
colour ="grey"),
panel.grid.major.x = element_blank(),
text = element_text(size=12),
axis.text=element_text(size=8))
#donut plot for the whole genome
perc_all <- perc %>% group_by(annotated) %>% summarize(n=n()) %>% mutate(perc=(100*n)/sum(n))
perc_all$ymax <- cumsum(perc_all$perc)
# Compute the bottom of each rectangle
perc_all$ymin <- c(0, head(perc_all$ymax, n=-1))
# Compute label position
perc_all$labelPosition <- (perc_all$ymax + perc_all$ymin) / 2
# Compute a good label
perc_all$label <- paste0(round(perc_all$perc,0), "%")
# Make the plot
all_plot<-ggplot(perc_all, aes(ymax=ymax, ymin=ymin, xmax=4, xmin=3, fill=annotated)) +
geom_rect() +
geom_text( x=3.5, aes(y=labelPosition, label=label,color=annotated), size=8) +
scale_fill_manual(values = c("Non-annotated"="#ffda73","Annotated"="#156902"))+
scale_color_manual(values = c("Non-annotated"="#156902","Annotated"="#ffda73"))+
coord_polar(theta="y") + ggtitle("Whole transcriptome (n = 11,185)")+
xlim(c(2, 4)) +
theme_void() +
theme(legend.position = "none",text = element_text(size=12))
library(patchwork)
dge_plot+all_plot
all_plot<-ggplot(perc_all, aes(ymax=ymax, ymin=ymin, xmax=4, xmin=3, fill=annotated)) +
geom_rect() +
geom_text( x=3.5, aes(y=labelPosition, label=label,color=annotated), size=2.75) +
scale_fill_manual(values = c("Non-annotated"="#ffda73","Annotated"="#156902"))+
scale_color_manual(values = c("Non-annotated"="#156902","Annotated"="#ffda73"))+
coord_polar(theta="y") + ggtitle("Whole transcriptome (n = 11,185)")+
xlim(c(2, 4)) +
theme_void() +
theme(legend.position = "none",text = element_text(size=8),plot.title = element_text(size=8))
dge_plot<-ggplot(perc_dge %>% filter(gene_set %in% c("Upregulated in culture","Upregulated in lichen")),
aes(x=gene_set,y=n,fill=annotated))+geom_bar(position="stack",stat="identity")+
geom_text(aes(label = paste0(round(perc,0),"%"),color=annotated), position=position_stack(vjust = 0.5),size=2.75)+
xlab("")+ylab("# of transcripts")+ggtitle("Differentially expressed")+
scale_fill_manual(values = c("Non-annotated"="#ffda73","Annotated"="#156902"))+
scale_color_manual(values = c("Non-annotated"="#156902","Annotated"="#ffda73"))+ theme_minimal()+
theme(legend.title=element_blank(),legend.position = c(0.2, 0.8),
legend.background = element_rect(fill="white",
linewidth=0.5, linetype="solid",
colour ="grey"),
panel.grid.major.x = element_blank(),
text = element_text(size=8),
axis.text=element_text(size=6),plot.title = element_text(size=8))
pdf(file="../results/annotated_percent.pdf",width=4.5,height=3.5)
dge_plot+all_plot
dev.off()
## quartz_off_screen
## 2
lichen_unique<-counts_tab %>% filter(XBC2>0,XBA1>0,XSA2_2>0,XSC1>0,XSE2>0,XBE1>0,XTA2>0,XSC2>0,
XSA2>0,XBA2>0,XBC1>0,XTA1>0,XSA1>0,XTC2>0,XTE2>0,XBE2>0,XMC2>0,
S_21XB1==0,KS21XB1==0,S_21XB3==0,S_42XB1==0,S_42XB2==0,S_42XB3==0,
KS48XB1==0,KS48XB2==0,KS48XB3==0,KS9XB1==0,KS9XB2==0,KS9XB3==0) %>%
pivot_longer(-target_id,names_to="sample",values_to="counts") %>%
filter(counts>0, sample !="MP_I",sample !="MP_II") %>% group_by(target_id) %>% summarise(avg_counts_lichen=mean(as.numeric(counts))) %>%
left_join(funannot, by=c("target_id"="TranscriptID")) %>%
select(-c(CDS.transcript,Translation,gDNA,mRNA))
lichen_unique %>%
kable(format = "html", col.names = colnames(lichen_unique)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | avg_counts_lichen | GeneID | Feature | Contig | Start | Stop | Strand | Name | Product | Alias.Synonyms | EC_number | BUSCO | PFAM | InterPro | EggNog | COG | GO.Terms | Secreted | Membrane | Protease | CAZyme | antiSMASH | Notes | ProtID | CAZyme_new | COG_new | EggNog_new | GO.Terms_new | InterPro_new | PFAM_new | Protease_new | Secreted_new | KO |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_001612-T1 | 46.99245 | XANPAGTX0501_001612 | mRNA | Xp_GTX0501_2 | 2002693 | 2003141 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_001612_T1_XANPAGTX0501_001612 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_002783-T1 | 18.68803 | XANPAGTX0501_002783 | mRNA | Xp_GTX0501_4 | 808460 | 808865 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_002783_T1_XANPAGTX0501_002783 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_003199-T1 | 20.17647 | XANPAGTX0501_003199 | mRNA | Xp_GTX0501_5 | 87909 | 89177 |
|
AIM6_3 | Altered inheritance of mitochondria protein 6 | NA | NA | NA | NA | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily;IPR039559 Altered inheritance of mitochondria protein 6, PI-PLC-like catalytic domain | ENOG503NZFJ | S:(S) Function unknown | GO_function: GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA];GO_process: GO:0006629 - lipid metabolic process [Evidence IEA] | NA | NA | NA | NA | Cluster_2 | NA | XANPAGTX0501_003199_T1_XANPAGTX0501_003199 | NA | S:(S) Function unknown | ENOG503NZFJ | GO_function: GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA], GO_process: GO:0006629 - lipid metabolic process [Evidence IEA] | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily, IPR039559 Altered inheritance of mitochondria protein 6, PI-PLC-like catalytic domain | NA | NA | NA | |
| XANPAGTX0501_006970-T1 | 48.17647 | XANPAGTX0501_006970 | mRNA | Xp_GTX0501_11 | 354394 | 354648 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_006970_T1_XANPAGTX0501_006970 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_006972-T1 | 74.64706 | XANPAGTX0501_006972 | mRNA | Xp_GTX0501_11 | 357523 | 357828 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_006972_T1_XANPAGTX0501_006972 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_008008-T1 | 58.88235 | XANPAGTX0501_008008 | mRNA | Xp_GTX0501_14 | 138465 | 139439 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_008008_T1_XANPAGTX0501_008008 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_008856-T1 | 94.82353 | XANPAGTX0501_008856 | mRNA | Xp_GTX0501_17 | 399345 | 400886 |
|
NA | hypothetical protein | NA | NA | NA | NA | IPR032675 Leucine-rich repeat domain superfamily | NA | NA | NA | NA | NA | NA | NA | Cluster_1 | NA | XANPAGTX0501_008856_T1_XANPAGTX0501_008856 | NA | NA | ENOG503P83U | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily | NA | NA | NA | |
| XANPAGTX0501_009040-T1 | 57.41176 | XANPAGTX0501_009040 | mRNA | Xp_GTX0501_18 | 366441 | 366695 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_009040_T1_XANPAGTX0501_009040 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_009438-T1 | 963.88235 | XANPAGTX0501_009438 | mRNA | Xp_GTX0501_21 | 196714 | 197521 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_009438_T1_XANPAGTX0501_009438 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_009555-T1 | 1952.88235 | XANPAGTX0501_009555 | mRNA | Xp_GTX0501_22 | 191143 | 191546 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_009555_T1_XANPAGTX0501_009555 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_009582-T1 | 17.00000 | XANPAGTX0501_009582 | mRNA | Xp_GTX0501_22 | 265438 | 265938 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_009582_T1_XANPAGTX0501_009582 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_009957-T1 | 69.00000 | XANPAGTX0501_009957 | mRNA | Xp_GTX0501_27 | 408 | 679 |
|
NA | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Cluster_1 | NA | XANPAGTX0501_009957_T1_XANPAGTX0501_009957 | NA | NA | NA | NA | NA | NA | NA | NA | |
| XANPAGTX0501_010684-T1 | 45.11765 | XANPAGTX0501_010684 | mRNA | Xp_GTX0501_46 | 20975 | 22156 |
|
NA | hypothetical protein | NA | NA | NA | PF00067 | IPR001128 Cytochrome P450;IPR002401 Cytochrome P450, E-class, group I;IPR017972 Cytochrome P450, conserved site;IPR036396 Cytochrome P450 superfamily | ENOG503NWJC | Q:(Q) Secondary metabolites biosynthesis, transport and catabolism | GO_function: GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA];GO_function: GO:0020037 - heme binding [Evidence IEA];GO_function: GO:0005506 - iron ion binding [Evidence IEA];GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | NA | NA | NA | NA | NA | NA | XANPAGTX0501_010684_T1_XANPAGTX0501_010684 | NA | Q:(Q) Secondary metabolites biosynthesis, transport and catabolism | ENOG503NWJC | GO_function: GO:0005506 - iron ion binding [Evidence IEA], GO_function: GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA], GO_function: GO:0020037 - heme binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR001128 Cytochrome P450, IPR002401 Cytochrome P450, E-class, group I, IPR017972 Cytochrome P450, conserved site, IPR036396 Cytochrome P450 superfamily | PF00067 | NA | NA |
act as scavengers in the cell, collecting “junk” proteins to deliver to a “waste processor,” called the SCF complex, to which they dock through their F-box domain. In the SCF complex, the junk proteins are marked with ubiquitin for “incineration” in the proteasome. F-box proteins do not act indiscriminately but recruit specific, often modified proteins to the SCF complex and in this way regulate the level of certain proteins in a cell. F-box proteins are found in all eukaryotes and display a large variety of functions. In fungi they are, for example, involved in control of the cell division cycle, glucose sensing, mitochondrial connectivity, and control of the circadian clock
plot_bootstrap(so,
target_id = "XANPAGTX0501_008856-T1",
units = "est_counts",
color_by = "condition")
culture_unique<-counts_tab %>% filter(XBC2==0,XBA1==0,XSA2_2==0,XSC1==0,XSE2==0,XBE1==0,XTA2==0,XSC2==0,
XSA2==0,XBA2==0,XBC1==0,XTA1==0,XSA1==0,XTC2==0,XTE2==0,XBE2==0,XMC2==0,
S_21XB1>0,KS21XB1>0,S_21XB3>0,S_42XB1>0,S_42XB2>0,S_42XB3>0,
KS48XB1>0,KS48XB2>0,KS48XB3>0,KS9XB1>0,KS9XB2>0,KS9XB3>0) %>% pivot_longer(-target_id,names_to="sample",values_to="counts") %>%
filter(counts>0, sample !="MP_I",sample !="MP_II") %>% group_by(target_id) %>% summarise(avg_counts_culture=mean(as.numeric(counts))) %>%
left_join(funannot, by=c("target_id"="TranscriptID")) %>%
select(-c(CDS.transcript,Translation,gDNA,mRNA))
culture_unique %>%
kable(format = "html", col.names = colnames(culture_unique)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | avg_counts_culture | GeneID | Feature | Contig | Start | Stop | Strand | Name | Product | Alias.Synonyms | EC_number | BUSCO | PFAM | InterPro | EggNog | COG | GO.Terms | Secreted | Membrane | Protease | CAZyme | antiSMASH | Notes | ProtID | CAZyme_new | COG_new | EggNog_new | GO.Terms_new | InterPro_new | PFAM_new | Protease_new | Secreted_new | KO |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_008359-T2 | 967.2169 | XANPAGTX0501_008359 | mRNA | Xp_GTX0501_15 | 271800 | 273051 |
|
NA | hypothetical protein | NA | NA | NA | PF03881 | IPR011009 Protein kinase-like domain superfamily;IPR016477 Fructosamine/Ketosamine-3-kinase | ENOG503P2EP | G:(G) Carbohydrate transport and metabolism | NA | NA | NA | NA | NA | NA | NA | XANPAGTX0501_008359_T2_XANPAGTX0501_008359 | NA | G:(G) Carbohydrate transport and metabolism | ENOG503NZHR, ENOG503P2EP | NA | IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase | PF03881 | NA | NA |
plot_bootstrap(so,
target_id = "XANPAGTX0501_002103-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_002104-T1",
units = "est_counts",
color_by = "condition")
galpha<-funannot %>% filter(grepl("IPR001019",InterPro_new))
sig %>% filter(target_id %in% galpha$TranscriptID)
## # A tibble: 5 × 12
## target_id pval qval b se_b mean_obs var_obs tech_var sigma_sq
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 XANPAGTX050… 2.19e-14 3.18e-13 0.625 0.0819 8.08 0.130 0.000966 0.0323
## 2 XANPAGTX050… 6.74e- 9 4.96e- 8 0.582 0.100 7.59 0.153 0.000548 0.0702
## 3 XANPAGTX050… 4.12e- 4 1.26e- 3 0.491 0.139 7.97 0.192 0.00126 0.135
## 4 XANPAGTX050… 2.57e- 3 6.48e- 3 0.233 0.0771 7.46 0.0288 0.000600 0.0152
## 5 XANPAGTX050… 2.58e- 2 4.90e- 2 0.210 0.0941 7.16 0.0712 0.000799 0.0615
## # ℹ 3 more variables: smooth_sigma_sq <dbl>, final_sigma_sq <dbl>, change <chr>
../02_mycobiont_genome/notebook/09_lichen_specific_genes.htmlfunannot2<-read.delim2("../../02_mycobiont_genome/analysis_and_temp_files/09_ortho/lichen_enriched_ortho_in_xanpa.tsv",sep="\t")
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_lichen_enriched_all.png",res=300,width=2000,height=1500)
plot_transcript_heatmap(so, transcripts=funannot2$TranscriptID[funannot2$lichen_ortho==T],
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_lichen_enriched_all.png")
og_sig<-sig %>% filter(target_id %in% funannot2$TranscriptID[funannot2$lichen_ortho==T])
og_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 97
## 2 lichen 264
## 3 low_logFC 374
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_lichen_enriched_dge.png",res=300,width=2000,height=1000)
plot_transcript_heatmap(so, transcripts=og_sig$target_id[og_sig$change!="low_logFC"],
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_lichen_enriched_dge.png")
funannot2 %>% group_by(antiSMASH,Contig) %>% summarize(n=n()) %>% filter(!is.na(antiSMASH))
## `summarise()` has grouped output by 'antiSMASH'. You can override using the
## `.groups` argument.
## # A tibble: 59 × 3
## # Groups: antiSMASH [7]
## antiSMASH Contig n
## <chr> <chr> <int>
## 1 Cluster_1 Xp_GTX0501_1 39
## 2 Cluster_1 Xp_GTX0501_10 20
## 3 Cluster_1 Xp_GTX0501_11 15
## 4 Cluster_1 Xp_GTX0501_12 12
## 5 Cluster_1 Xp_GTX0501_13 24
## 6 Cluster_1 Xp_GTX0501_14 11
## 7 Cluster_1 Xp_GTX0501_15 18
## 8 Cluster_1 Xp_GTX0501_17 24
## 9 Cluster_1 Xp_GTX0501_2 41
## 10 Cluster_1 Xp_GTX0501_24 44
## # ℹ 49 more rows
sm_genes<-funannot2 %>% filter(!is.na(antiSMASH)) %>% mutate(cluster = paste0(Contig,"_",antiSMASH)) %>% select(-c(gDNA,mRNA,CDS.transcript,Translation,CAZyme,COG,EggNog,GO.Terms,InterPro,PFAM,Protease,Secreted))
sm_sig<-sig %>% filter(target_id %in% sm_genes$TranscriptID)
sm_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 96
## 2 lichen 222
## 3 low_logFC 379
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_SM_dge.png",res=300,width=2000,height=1000)
plot_transcript_heatmap(so, transcripts=sm_sig$target_id[sm_sig$change!="low_logFC"],
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_SM_dge.png")
library(splitstackshape)
antismash<-read.delim2("../../02_mycobiont_genome/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_pred/antismash/antismash_summary.txt")
#get a list of all genes in each cluster
antismash_gene_all<-antismash %>% mutate(start_num=as.numeric(gsub("^.*?_","",Start)),
end_num=as.numeric(gsub("^.*?_","",End))) %>%
mutate(gene_number=end_num-start_num+1) %>%
expandRows("gene_number", drop = FALSE) %>%
group_by(start_num,end_num) %>%
mutate(gene_num = seq(start_num[1],end_num[1],by = 1)) %>%
mutate(GeneID=ifelse(gene_num<1000,paste0("XANPAGTX0501_000",gene_num),
ifelse(gene_num<10000,paste0("XANPAGTX0501_00",gene_num),
paste0("XANPAGTX0501_0",gene_num)))) %>%
mutate(Core_gene = ifelse(GeneID==Core_gene1|GeneID==Core_gene2,T,F)) %>% ungroup %>%
select(GeneID,Cluster,Description,Core_gene)
#add transcriptomic results
summary_antismash_all<-antismash_gene_all %>% left_join(funannot2,relationship = "many-to-many") %>%
left_join(sig, by = c("TranscriptID"="target_id")) %>%
group_by(Cluster,change) %>% summarize(n=n()) %>%
pivot_wider(names_from=change,values_from=n,values_fill=0) %>%
left_join(antismash)
## Joining with `by = join_by(GeneID)`
## `summarise()` has grouped output by 'Cluster'. You can override using the
## `.groups` argument.
## Joining with `by = join_by(Cluster)`
summary_antismash_core<-antismash_gene_all %>% filter(Core_gene==T) %>%
left_join(funannot2,relationship = "many-to-many") %>%
left_join(sig, by = c("TranscriptID"="target_id")) %>%
mutate(change=ifelse(change %in% c("lichen","culture"),change,"Non-DGE")) %>%
group_by(Cluster) %>% mutate(Core_gene_status=paste(change,collapse=",")) %>%
select(Cluster,Core_gene_status) %>% distinct()
## Joining with `by = join_by(GeneID)`
summary_antismash_core %>% group_by(Core_gene_status) %>%summarize(n=n())
## # A tibble: 6 × 2
## Core_gene_status n
## <chr> <int>
## 1 Non-DGE 35
## 2 Non-DGE,Non-DGE 2
## 3 culture 6
## 4 culture,culture 1
## 5 lichen 14
## 6 lichen,Non-DGE 1
summary_antismash_all<-summary_antismash_all %>% left_join(summary_antismash_core)
## Joining with `by = join_by(Cluster)`
summary_antismash_all %>%
kable(format = "html", col.names = colnames(summary_antismash_all)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| Cluster | culture | lichen | low_logFC | NA | Description | Start | End | Core_gene1 | Core_gene2 | KnownClusterBlast_MIBIG | KnownClusterBlast_description | KnownClusterBlast_Similarity | KnownClusterBlast_includes_core | Core_gene_status |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Xp_GTX0501_10_Cluster_1 | 2 | 12 | 4 | 2 | NRPS-like | XANPAGTX0501_006291 | XANPAGTX0501_006310 | XANPAGTX0501_006297 | NA | Non-DGE | ||||
| Xp_GTX0501_10_Cluster_2 | 2 | 9 | 6 | 8 | T1PKS | XANPAGTX0501_006308 | XANPAGTX0501_006332 | XANPAGTX0501_006319 | BGC0002215 | HEx-pks23 polyketide<ca> | 0.22 | 1 | lichen | |
| Xp_GTX0501_10_Cluster_3 | 0 | 2 | 14 | 11 | NRPS-like | XANPAGTX0501_006344 | XANPAGTX0501_006369 | XANPAGTX0501_006358 | NA | Non-DGE | ||||
| Xp_GTX0501_10_Cluster_4 | 2 | 1 | 14 | 9 | T3PKS | XANPAGTX0501_006734 | XANPAGTX0501_006757 | XANPAGTX0501_006744 | NA | Non-DGE | ||||
| Xp_GTX0501_11_Cluster_1 | 3 | 2 | 2 | 7 | NRPS | XANPAGTX0501_006840 | XANPAGTX0501_006853 | XANPAGTX0501_006845 | BGC0002235 | ACE1 | 0.11 | 1 | lichen | |
| Xp_GTX0501_12_Cluster_1 | 1 | 4 | 2 | 5 | T1PKS | XANPAGTX0501_007263 | XANPAGTX0501_007274 | XANPAGTX0501_007266 | BGC0000146 | solanapyrone D | 0.33 | 1 | Non-DGE | |
| Xp_GTX0501_12_Cluster_2 | 0 | 9 | 12 | 11 | T1PKS | XANPAGTX0501_007334 | XANPAGTX0501_007363 | XANPAGTX0501_007346 | NA | Non-DGE,Non-DGE | ||||
| Xp_GTX0501_12_Cluster_3 | 3 | 1 | 4 | 5 | terpene | XANPAGTX0501_007388 | XANPAGTX0501_007400 | XANPAGTX0501_007395 | NA | Non-DGE | ||||
| Xp_GTX0501_13_Cluster_1 | 1 | 5 | 2 | 14 | NRPS-like | XANPAGTX0501_007869 | XANPAGTX0501_007889 | XANPAGTX0501_007880 | NA | Non-DGE | ||||
| Xp_GTX0501_14_Cluster_1 | 1 | 2 | 4 | 3 | terpene | XANPAGTX0501_007984 | XANPAGTX0501_007993 | XANPAGTX0501_007988 | NA | Non-DGE | ||||
| Xp_GTX0501_15_Cluster_1 | 1 | 7 | 8 | 3 | NRPS-like | XANPAGTX0501_008267 | XANPAGTX0501_008284 | XANPAGTX0501_008272 | NA | lichen | ||||
| Xp_GTX0501_17_Cluster_1 | 0 | 7 | 8 | 7 | T1PKS | XANPAGTX0501_008845 | XANPAGTX0501_008866 | XANPAGTX0501_008852 | BGC0000156 |
TAN-1612 biosynthetic gene cluster from |
0.6 | 1 | lichen | |
| Xp_GTX0501_1_Cluster_1 | 5 | 6 | 12 | 15 | fungal-RiPP-like | XANPAGTX0501_000667 | XANPAGTX0501_000702 | XANPAGTX0501_000685 | NA | lichen | ||||
| Xp_GTX0501_1_Cluster_2 | 1 | 7 | 4 | 14 | T1PKS | XANPAGTX0501_000912 | XANPAGTX0501_000937 | XANPAGTX0501_000926 | BGC0000146 | solanapyrone D | 0.5 | 0 | Non-DGE | |
| Xp_GTX0501_24_Cluster_1 | 10 | 10 | 7 | 17 | fungal-RiPP-like | XANPAGTX0501_009693 | XANPAGTX0501_009736 | XANPAGTX0501_009715 | XANPAGTX0501_009716 | NA | culture,culture | |||
| Xp_GTX0501_25_Cluster_1 | 0 | 2 | 4 | 11 | terpene | XANPAGTX0501_009858 | XANPAGTX0501_009874 | XANPAGTX0501_009866 | NA | Non-DGE | ||||
| Xp_GTX0501_27_Cluster_1 | 1 | 2 | 12 | 7 | NRPS-like | XANPAGTX0501_009956 | XANPAGTX0501_009977 | XANPAGTX0501_009964 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_1 | 2 | 6 | 15 | 16 | fungal-RiPP-like | XANPAGTX0501_001046 | XANPAGTX0501_001083 | XANPAGTX0501_001064 | NA | lichen | ||||
| Xp_GTX0501_2_Cluster_2 | 1 | 3 | 10 | 14 | NRPS | XANPAGTX0501_001225 | XANPAGTX0501_001250 | XANPAGTX0501_001239 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_3 | 1 | 1 | 8 | 14 | NRPS-like | XANPAGTX0501_001291 | XANPAGTX0501_001314 | XANPAGTX0501_001305 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_4 | 0 | 0 | 7 | 6 | terpene | XANPAGTX0501_001616 | XANPAGTX0501_001628 | XANPAGTX0501_001622 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_5 | 0 | 2 | 3 | 18 | T1PKS | XANPAGTX0501_001669 | XANPAGTX0501_001691 | XANPAGTX0501_001679 | NA | Non-DGE | ||||
| Xp_GTX0501_2_Cluster_6 | 0 | 0 | 5 | 19 | NRP-metallophore | XANPAGTX0501_001682 | XANPAGTX0501_001705 | XANPAGTX0501_001696 | XANPAGTX0501_001694 | NA | Non-DGE,Non-DGE | |||
| Xp_GTX0501_2_Cluster_7 | 0 | 0 | 5 | 16 | NRPS | XANPAGTX0501_001682 | XANPAGTX0501_001702 | XANPAGTX0501_001694 | NA | Non-DGE | ||||
| Xp_GTX0501_35_Cluster_1 | 6 | 3 | 3 | 9 | NRPS-like | XANPAGTX0501_010404 | XANPAGTX0501_010423 | XANPAGTX0501_010409 | NA | culture | ||||
| Xp_GTX0501_35_Cluster_2 | 2 | 8 | 4 | 9 | T1PKS | XANPAGTX0501_010418 | XANPAGTX0501_010440 | XANPAGTX0501_010430 | NA | lichen | ||||
| Xp_GTX0501_36_Cluster_1 | 2 | 4 | 9 | 11 | T1PKS | XANPAGTX0501_010449 | XANPAGTX0501_010474 | XANPAGTX0501_010464 | BGC0001242 | oxyjavanicin | 0.25 | 1 | Non-DGE | |
| Xp_GTX0501_3_Cluster_1 | 10 | 8 | 0 | 3 | NRPS | XANPAGTX0501_001961 | XANPAGTX0501_001981 | XANPAGTX0501_001972 | BGC0001741 | phyllostictine A/phyllostictine B | 0.5 | 1 | culture | |
| Xp_GTX0501_3_Cluster_2 | 10 | 6 | 0 | 4 | T1PKS | XANPAGTX0501_001963 | XANPAGTX0501_001982 | XANPAGTX0501_001973 | BGC0001741 | phyllostictine A/phyllostictine B | 0.5 | 1 | culture | |
| Xp_GTX0501_3_Cluster_3 | 0 | 7 | 1 | 6 | terpene | XANPAGTX0501_002180 | XANPAGTX0501_002193 | XANPAGTX0501_002188 | NA | Non-DGE | ||||
| Xp_GTX0501_41_Cluster_1 | 0 | 1 | 9 | 3 | NRPS-like | XANPAGTX0501_010609 | XANPAGTX0501_010621 | XANPAGTX0501_010621 | NA | lichen | ||||
| Xp_GTX0501_43_Cluster_1 | 0 | 4 | 4 | 16 | T1PKS | XANPAGTX0501_010622 | XANPAGTX0501_010644 | XANPAGTX0501_010632 | NA | Non-DGE | ||||
| Xp_GTX0501_48_Cluster_1 | 3 | 6 | 2 | 8 | NRPS-like | XANPAGTX0501_010686 | XANPAGTX0501_010704 | XANPAGTX0501_010692 | NA | culture | ||||
| Xp_GTX0501_4_Cluster_1 | 1 | 0 | 3 | 9 | terpene | XANPAGTX0501_002454 | XANPAGTX0501_002466 | XANPAGTX0501_002460 | NA | Non-DGE | ||||
| Xp_GTX0501_4_Cluster_2 | 0 | 6 | 15 | 12 | NRPS-like | XANPAGTX0501_002475 | XANPAGTX0501_002501 | XANPAGTX0501_002488 | NA | lichen | ||||
| Xp_GTX0501_4_Cluster_3 | 0 | 1 | 6 | 7 | terpene | XANPAGTX0501_002520 | XANPAGTX0501_002531 | XANPAGTX0501_002527 | BGC0001839 | squalestatin S1 | 0.4 | 1 | Non-DGE | |
| Xp_GTX0501_4_Cluster_4 | 0 | 3 | 10 | 13 | NRPS | XANPAGTX0501_002525 | XANPAGTX0501_002549 | XANPAGTX0501_002535 | BGC0002164 | peramine | 1 | 1 | lichen | |
| Xp_GTX0501_4_Cluster_5 | 0 | 3 | 5 | 17 | NRPS | XANPAGTX0501_003108 | XANPAGTX0501_003131 | XANPAGTX0501_003119 | NA | lichen | ||||
| Xp_GTX0501_50_Cluster_1 | 0 | 2 | 1 | 3 | T1PKS | XANPAGTX0501_010705 | XANPAGTX0501_010710 | XANPAGTX0501_010709 | BGC0000146 | solanapyrone D | 0.33 | 1 | Non-DGE | |
| Xp_GTX0501_52_Cluster_1 | 2 | 3 | 1 | 2 | NRPS | XANPAGTX0501_010711 | XANPAGTX0501_010717 | XANPAGTX0501_010715 | NA | Non-DGE | ||||
| Xp_GTX0501_5_Cluster_1 | 4 | 5 | 2 | 9 | T1PKS | XANPAGTX0501_003170 | XANPAGTX0501_003189 | XANPAGTX0501_003176 | BGC0002515 | solanapyrone A | 0.4 | 1 | culture | |
| Xp_GTX0501_5_Cluster_2 | 7 | 5 | 7 | 7 | T1PKS | XANPAGTX0501_003179 | XANPAGTX0501_003204 | XANPAGTX0501_003194 | NA | Non-DGE | ||||
| Xp_GTX0501_5_Cluster_3 | 0 | 3 | 7 | 16 | NRPS,T1PKS | XANPAGTX0501_003287 | XANPAGTX0501_003311 | XANPAGTX0501_003300 | BGC0001067 | fumagillin/_-trans-bergamotene/fumagillol | 0.2 | 0 | Non-DGE | |
| Xp_GTX0501_5_Cluster_4 | 2 | 2 | 11 | 13 | NRPS-like | XANPAGTX0501_003361 | XANPAGTX0501_003388 | XANPAGTX0501_003374 | NA | lichen | ||||
| Xp_GTX0501_6_Cluster_1 | 0 | 3 | 10 | 10 | T1PKS | XANPAGTX0501_004370 | XANPAGTX0501_004390 | XANPAGTX0501_004380 | NA | Non-DGE | ||||
| Xp_GTX0501_6_Cluster_2 | 0 | 4 | 7 | 13 | T1PKS | XANPAGTX0501_004397 | XANPAGTX0501_004420 | XANPAGTX0501_004410 | NA | Non-DGE | ||||
| Xp_GTX0501_7_Cluster_1 | 0 | 4 | 10 | 12 | T1PKS | XANPAGTX0501_004611 | XANPAGTX0501_004634 | XANPAGTX0501_004622 | BGC0001258 | 1,3,6,8-tetrahydroxynaphthalene | 1 | 1 | Non-DGE | |
| Xp_GTX0501_7_Cluster_2 | 0 | 2 | 7 | 3 | terpene | XANPAGTX0501_004765 | XANPAGTX0501_004776 | XANPAGTX0501_004770 | NA | lichen | ||||
| Xp_GTX0501_7_Cluster_3 | 1 | 9 | 9 | 13 | T1PKS | XANPAGTX0501_005055 | XANPAGTX0501_005086 | XANPAGTX0501_005070 | NA | Non-DGE | ||||
| Xp_GTX0501_7_Cluster_4 | 1 | 7 | 7 | 10 | NRPS-like | XANPAGTX0501_005071 | XANPAGTX0501_005095 | XANPAGTX0501_005087 | NA | Non-DGE | ||||
| Xp_GTX0501_7_Cluster_5 | 1 | 8 | 7 | 8 | T1PKS | XANPAGTX0501_005075 | XANPAGTX0501_005098 | XANPAGTX0501_005090 | NA | Non-DGE | ||||
| Xp_GTX0501_8_Cluster_1 | 9 | 0 | 4 | 11 | NRPS | XANPAGTX0501_005105 | XANPAGTX0501_005128 | XANPAGTX0501_005116 | NA | culture | ||||
| Xp_GTX0501_8_Cluster_2 | 1 | 6 | 9 | 13 | T1PKS | XANPAGTX0501_005240 | XANPAGTX0501_005265 | XANPAGTX0501_005252 | NA | lichen | ||||
| Xp_GTX0501_8_Cluster_3 | 1 | 5 | 10 | 13 | T1PKS | XANPAGTX0501_005280 | XANPAGTX0501_005306 | XANPAGTX0501_005291 | BGC0000046 | depudecin | 0.33 | 0 | Non-DGE | |
| Xp_GTX0501_8_Cluster_4 | 5 | 4 | 11 | 15 | fungal-RiPP-like | XANPAGTX0501_005329 | XANPAGTX0501_005361 | XANPAGTX0501_005349 | NA | Non-DGE | ||||
| Xp_GTX0501_8_Cluster_5 | 1 | 3 | 4 | 5 | terpene | XANPAGTX0501_005377 | XANPAGTX0501_005388 | XANPAGTX0501_005382 | NA | lichen,Non-DGE | ||||
| Xp_GTX0501_9_Cluster_1 | 0 | 4 | 3 | 14 | T1PKS | XANPAGTX0501_005732 | XANPAGTX0501_005752 | XANPAGTX0501_005742 | BGC0001258 | 1,3,6,8-tetrahydroxynaphthalene | 1 | 1 | Non-DGE | |
| Xp_GTX0501_9_Cluster_2 | 2 | 0 | 5 | 16 | NRPS | XANPAGTX0501_005742 | XANPAGTX0501_005764 | XANPAGTX0501_005751 | NA | Non-DGE | ||||
| Xp_GTX0501_9_Cluster_3 | 2 | 3 | 12 | 11 | T1PKS | XANPAGTX0501_005922 | XANPAGTX0501_005948 | XANPAGTX0501_005935 | BGC0002194 | epipyrone A | 0.75 | 1 | Non-DGE |
summary_antismash_all %>% filter(culture==0,lichen>0,grepl("lichen",Core_gene_status)) %>%
kable(format = "html", col.names = colnames(summary_antismash_all)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| Cluster | culture | lichen | low_logFC | NA | Description | Start | End | Core_gene1 | Core_gene2 | KnownClusterBlast_MIBIG | KnownClusterBlast_description | KnownClusterBlast_Similarity | KnownClusterBlast_includes_core | Core_gene_status |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Xp_GTX0501_17_Cluster_1 | 0 | 7 | 8 | 7 | T1PKS | XANPAGTX0501_008845 | XANPAGTX0501_008866 | XANPAGTX0501_008852 | BGC0000156 |
TAN-1612 biosynthetic gene cluster from |
0.6 | 1 | lichen | |
| Xp_GTX0501_41_Cluster_1 | 0 | 1 | 9 | 3 | NRPS-like | XANPAGTX0501_010609 | XANPAGTX0501_010621 | XANPAGTX0501_010621 | NA | lichen | ||||
| Xp_GTX0501_4_Cluster_2 | 0 | 6 | 15 | 12 | NRPS-like | XANPAGTX0501_002475 | XANPAGTX0501_002501 | XANPAGTX0501_002488 | NA | lichen | ||||
| Xp_GTX0501_4_Cluster_4 | 0 | 3 | 10 | 13 | NRPS | XANPAGTX0501_002525 | XANPAGTX0501_002549 | XANPAGTX0501_002535 | BGC0002164 | peramine | 1 | 1 | lichen | |
| Xp_GTX0501_4_Cluster_5 | 0 | 3 | 5 | 17 | NRPS | XANPAGTX0501_003108 | XANPAGTX0501_003131 | XANPAGTX0501_003119 | NA | lichen | ||||
| Xp_GTX0501_7_Cluster_2 | 0 | 2 | 7 | 3 | terpene | XANPAGTX0501_004765 | XANPAGTX0501_004776 | XANPAGTX0501_004770 | NA | lichen |
sig %>% filter(target_id %in% c("XANPAGTX0501_008850-T1","XANPAGTX0501_008851-T1","XANPAGTX0501_008852-T1","XANPAGTX0501_008853-T1")) %>% select(target_id,qval,b,change)
## # A tibble: 4 × 4
## target_id qval b change
## <chr> <dbl> <dbl> <chr>
## 1 XANPAGTX0501_008850-T1 6.06e-22 -1.70 lichen
## 2 XANPAGTX0501_008851-T1 5.87e-21 -1.93 lichen
## 3 XANPAGTX0501_008852-T1 1.87e-22 -2.08 lichen
## 4 XANPAGTX0501_008853-T1 3.26e-69 -4.00 lichen
plot_bootstrap(so,
target_id = "XANPAGTX0501_008850-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_008851-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_008852-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_008853-T1",
units = "est_counts",
color_by = "condition")
funannot2 %>% filter(grepl("IPR000719",InterPro)) %>% group_by(lichen_ortho) %>% summarize(n=n())
## # A tibble: 2 × 2
## lichen_ortho n
## <lgl> <int>
## 1 FALSE 115
## 2 TRUE 19
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR000719",InterPro)) %>% group_by(change) %>% summarize(n=n())
## # A tibble: 4 × 2
## change n
## <chr> <int>
## 1 culture 11
## 2 lichen 10
## 3 low_logFC 53
## 4 <NA> 60
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR008271",InterPro)) %>% group_by(change) %>% summarize(n=n())
## # A tibble: 4 × 2
## change n
## <chr> <int>
## 1 culture 9
## 2 lichen 4
## 3 low_logFC 42
## 4 <NA> 47
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR008271",InterPro),change %in% c("culture","lichen")) %>%
select(TranscriptID,b,change,Product,InterPro) %>%
kable(format = "html", col.names = c("TranscriptID","b","change","Product","InterPro")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | b | change | Product | InterPro |
|---|---|---|---|---|
| XANPAGTX0501_000131-T1 | 3.173122 | culture | hypothetical protein | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR011990 Tetratricopeptide-like helical domain superfamily;IPR017441 Protein kinase, ATP binding site |
| XANPAGTX0501_002130-T1 | 1.107301 | culture | hypothetical protein | IPR000719 Protein kinase domain;IPR001245 Serine-threonine/tyrosine-protein kinase, catalytic domain;IPR002110 Ankyrin repeat;IPR006597 Sel1-like repeat;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR011990 Tetratricopeptide-like helical domain superfamily;IPR020683 Domain of unknown function DUF3447;IPR036770 Ankyrin repeat-containing domain superfamily |
| XANPAGTX0501_002999-T3 | 1.110073 | culture | Serine/threonine-protein kinase, variant 3 | IPR000008 C2 domain;IPR000719 Protein kinase domain;IPR000961 AGC-kinase, C-terminal;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR017441 Protein kinase, ATP binding site;IPR017892 Protein kinase, C-terminal;IPR035892 C2 domain superfamily |
| XANPAGTX0501_003063-T3 | 1.307124 | culture | Cytochrome c oxidase subunit 1, variant 3 | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR017441 Protein kinase, ATP binding site |
| XANPAGTX0501_003150-T1 | 1.034833 | culture | hypothetical protein | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_003466-T1 | -1.376968 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_003979-T1 | 1.608051 | culture | Serine/threonine protein kinase | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR017441 Protein kinase, ATP binding site |
| XANPAGTX0501_004521-T1 | -1.452240 | lichen | hypothetical protein | IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_004525-T1 | -1.003000 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_005890-T1 | 1.279397 | culture | hypothetical protein | IPR000719 Protein kinase domain;IPR002110 Ankyrin repeat;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR020683 Domain of unknown function DUF3447;IPR036770 Ankyrin repeat-containing domain superfamily |
| XANPAGTX0501_006750-T1 | 1.049144 | culture | hypothetical protein | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_007777-T2 | 1.360843 | culture | eukaryotic translation initiation factor 2-alpha kinase | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR016255 eIF-2-alpha kinase Gcn2;IPR017441 Protein kinase, ATP binding site;IPR024435 Histidyl tRNA synthetase-related domain;IPR036621 Anticodon-binding domain superfamily;IPR041715 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain |
| XANPAGTX0501_010496-T1 | -3.360677 | lichen | MAP kinase-activated protein kinase 2 | IPR000253 Forkhead-associated (FHA) domain;IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR008984 SMAD/FHA domain superfamily;IPR011009 Protein kinase-like domain superfamily |
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR017240",InterPro)|grepl("IPR003527",InterPro) |
grepl( "IPR008352",InterPro) | grepl( "IPR038783",InterPro)) %>%
select(TranscriptID,b,change,Product,InterPro) %>%
kable(format = "html", col.names = c("TranscriptID","b","change","product","InterPro")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | b | change | product | InterPro |
|---|---|---|---|---|
| XANPAGTX0501_003276-T1 | -0.2487408 | low_logFC | mitogen-activated serine/threonine-protein kinase | IPR000719 Protein kinase domain;IPR003527 Mitogen-activated protein (MAP) kinase, conserved site;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR017441 Protein kinase, ATP binding site |
| XANPAGTX0501_003462-T1 | NA | NA | mitogen activated protein kinase | IPR000719 Protein kinase domain;IPR003527 Mitogen-activated protein (MAP) kinase, conserved site;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR017441 Protein kinase, ATP binding site |
| XANPAGTX0501_009386-T1 | NA | NA | Suppressor of Sensor Kinase (SLN1) | IPR000719 Protein kinase domain;IPR008271 Serine/threonine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily;IPR017240 Mitogen-activated protein (MAP) kinase kinase kinase Ssk2/Ssk22;IPR017441 Protein kinase, ATP binding site |
| XANPAGTX0501_010261-T1 | 0.5642185 | low_logFC | MAPK protein hog1 | IPR000719 Protein kinase domain;IPR003527 Mitogen-activated protein (MAP) kinase, conserved site;IPR008271 Serine/threonine-protein kinase, active site;IPR008352 Mitogen-activated protein (MAP) kinase p38-like;IPR011009 Protein kinase-like domain superfamily;IPR017441 Protein kinase, ATP binding site;IPR038783 Fungal mitogen-activated protein (MAP) kinase Sty1/Hog1 |
| XANPAGTX0501_010261-T2 | -0.4922589 | low_logFC | MAPK protein hog1, variant 2 | IPR000719 Protein kinase domain;IPR003527 Mitogen-activated protein (MAP) kinase, conserved site;IPR008271 Serine/threonine-protein kinase, active site;IPR008352 Mitogen-activated protein (MAP) kinase p38-like;IPR011009 Protein kinase-like domain superfamily;IPR017441 Protein kinase, ATP binding site;IPR038783 Fungal mitogen-activated protein (MAP) kinase Sty1/Hog1 |
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR000719",InterPro),change =="culture") %>%
filter(!grepl("IPR008271",InterPro)) %>%
select(TranscriptID,b,change,Product,InterPro) %>%
kable(format = "html", col.names = c("TranscriptID","b","change","product","InterPro")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | b | change | product | InterPro |
|---|---|---|---|---|
| XANPAGTX0501_000132-T1 | 3.167267 | culture | hypothetical protein | IPR000719 Protein kinase domain;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_005889-T1 | 3.211218 | culture | hypothetical protein | IPR000719 Protein kinase domain;IPR011009 Protein kinase-like domain superfamily |
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR000719",InterPro),change =="lichen") %>%
filter(!grepl("IPR008271",InterPro)) %>%
select(TranscriptID,b,change,Product,InterPro) %>%
kable(format = "html", col.names = c("TranscriptID","b","change","product","InterPro")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | b | change | product | InterPro |
|---|---|---|---|---|
| XANPAGTX0501_001006-T1 | -3.826268 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR011009 Protein kinase-like domain superfamily;IPR029498 Prion-inhibition and propagation, HeLo domain;IPR038305 HeLo domain superfamily |
| XANPAGTX0501_001007-T1 | -3.548226 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR002110 Ankyrin repeat;IPR011009 Protein kinase-like domain superfamily;IPR011990 Tetratricopeptide-like helical domain superfamily;IPR013026 None;IPR019734 Tetratricopeptide repeat;IPR020683 Domain of unknown function DUF3447;IPR036770 Ankyrin repeat-containing domain superfamily |
| XANPAGTX0501_004853-T1 | -1.196511 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR000961 AGC-kinase, C-terminal;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_009558-T1 | -1.573738 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR011009 Protein kinase-like domain superfamily;IPR036465 von Willebrand factor A-like domain superfamily |
| XANPAGTX0501_010435-T1 | -1.088118 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_010556-T1 | -2.886129 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR011009 Protein kinase-like domain superfamily |
| XANPAGTX0501_010558-T1 | -3.182102 | lichen | hypothetical protein | IPR000719 Protein kinase domain;IPR008266 Tyrosine-protein kinase, active site;IPR011009 Protein kinase-like domain superfamily |
funannot2 %>% filter(grepl("IPR005828",InterPro_new)) %>% group_by(lichen_ortho) %>% summarize(n=n())
## # A tibble: 2 × 2
## lichen_ortho n
## <lgl> <int>
## 1 FALSE 33
## 2 TRUE 5
funannot2 %>% filter(grepl("IPR005828",InterPro_new),lichen_ortho==T) %>% select(TranscriptID,InterPro_new)
## TranscriptID
## 1 XANPAGTX0501_001653-T1
## 2 XANPAGTX0501_005571-T1
## 3 XANPAGTX0501_005572-T1
## 4 XANPAGTX0501_008617-T1
## 5 XANPAGTX0501_010000-T1
## InterPro_new
## 1 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
## 2 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
## 3 IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
## 4 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
## 5 IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR005828",InterPro_new)) %>% group_by(change) %>% summarize(n=n())
## # A tibble: 4 × 2
## change n
## <chr> <int>
## 1 culture 2
## 2 lichen 6
## 3 low_logFC 16
## 4 <NA> 14
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR005828",InterPro_new),lichen_ortho==T) %>% group_by(change) %>% summarize(n=n())
## # A tibble: 2 × 2
## change n
## <chr> <int>
## 1 lichen 3
## 2 low_logFC 2
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR005828",InterPro_new),lichen_ortho==T) %>% select(TranscriptID,change,b,qval)
## TranscriptID change b qval
## 1 XANPAGTX0501_001653-T1 lichen -2.0408199 3.742386e-12
## 2 XANPAGTX0501_005571-T1 lichen -1.9797831 6.700776e-05
## 3 XANPAGTX0501_005572-T1 lichen -1.9025473 1.986579e-05
## 4 XANPAGTX0501_008617-T1 low_logFC -0.5728169 3.266494e-07
## 5 XANPAGTX0501_010000-T1 low_logFC -0.6135197 2.741270e-04
analysis_and_temp_files/08_dge_culture_lichen/blastp_polyol_transporters.txtsbatch --mem=5G -c 1 --wrap="source package d6092385-3a81-49d9-b044-8ffb85d0c446; blastp -query analysis_and_temp_files/08_dge_culture_lichen/polyol_transporters_genbank.fa -subject ../02_mycobiont_genome/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_pred/annotate_results/Xanthoria_parietina_GTX0501.proteins.fa -outfmt 6 -out analysis_and_temp_files/08_dge_culture_lichen/blastp_polyol_transporters.txt -evalue 1e-100"
polyol_blast<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/blastp_polyol_transporters.txt",header=F)
polyol_blast<-polyol_blast %>% select(V1,V2,V11,V12)
colnames(polyol_blast)<-c("query","subject","e-value","score")
polyol_blast
## query subject e-value score
## 1 AAX98668.1 XANPAGTX0501_010000-T1 1.49e-179 516
## 2 AAX98668.1 XANPAGTX0501_001653-T1 5.32e-176 508
## 3 AAX98668.1 XANPAGTX0501_008617-T1 2.52e-114 350
## 4 CAR65543.1 XANPAGTX0501_005996-T1 0.0 602
## 5 CAR65543.1 XANPAGTX0501_007564-T1 9.63e-178 519
## 6 CAR65543.1 XANPAGTX0501_009339-T1 5.39e-151 449
## 7 CAR65543.1 XANPAGTX0501_009339-T2 2.57e-149 442
## 8 CAR65543.1 XANPAGTX0501_000906-T1 4.21e-145 434
## 9 CAR65543.1 XANPAGTX0501_001701-T1 7.68e-133 402
## 10 CAG86001.1 XANPAGTX0501_005996-T1 0.0 591
## 11 CAG86001.1 XANPAGTX0501_007564-T1 2.80e-178 520
## 12 CAG86001.1 XANPAGTX0501_009339-T1 1.51e-152 453
## 13 CAG86001.1 XANPAGTX0501_009339-T2 2.52e-150 445
## 14 CAG86001.1 XANPAGTX0501_000906-T1 3.81e-146 436
## 15 CAG86001.1 XANPAGTX0501_001701-T1 1.48e-132 401
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(TranscriptID %in% polyol_blast$subject) %>% select(TranscriptID,change,b,qval,lichen_ortho)
## TranscriptID change b qval lichen_ortho
## 1 XANPAGTX0501_000906-T1 <NA> NA NA FALSE
## 2 XANPAGTX0501_001653-T1 lichen -2.0408199 3.742386e-12 TRUE
## 3 XANPAGTX0501_001701-T1 low_logFC 0.6237851 2.869476e-06 FALSE
## 4 XANPAGTX0501_005996-T1 low_logFC 0.4003563 2.088997e-06 FALSE
## 5 XANPAGTX0501_007564-T1 low_logFC 0.2966283 4.581743e-02 FALSE
## 6 XANPAGTX0501_008617-T1 low_logFC -0.5728169 3.266494e-07 TRUE
## 7 XANPAGTX0501_009339-T1 <NA> NA NA FALSE
## 8 XANPAGTX0501_009339-T2 <NA> NA NA FALSE
## 9 XANPAGTX0501_010000-T1 low_logFC -0.6135197 2.741270e-04 TRUE
plot_bootstrap(so,
target_id = "XANPAGTX0501_001653-T1",
units = "est_counts",
color_by = "condition")
funannot2 %>% filter(grepl("IPR001905",InterPro_new)) %>% group_by(lichen_ortho) %>% summarize(n=n())
## # A tibble: 1 × 2
## lichen_ortho n
## <lgl> <int>
## 1 FALSE 2
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR001905",InterPro_new)) %>% select(TranscriptID,change,b,qval)
## TranscriptID change b qval
## 1 XANPAGTX0501_004972-T1 lichen -2.248389 3.681322e-56
## 2 XANPAGTX0501_009385-T1 <NA> NA NA
transport_lic<-funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("transport",InterPro_new),change=="lichen") %>% select(TranscriptID,InterPro_new,lichen_ortho)
transport_lic %>%
kable(format = "html", col.names = c("TranscriptID","InterPro_new","lichen_ortho")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | InterPro_new | lichen_ortho |
|---|---|---|
| XANPAGTX0501_000142-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_000342-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_000342-T2 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_000684-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_000704-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_001082-T1 | IPR004853 Sugar phosphate transporter domain | FALSE |
| XANPAGTX0501_001448-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_001653-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_002486-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_003065-T3 | IPR005178 Organic solute transporter subunit alpha/Transmembrane protein 184 | FALSE |
| XANPAGTX0501_003337-T2 | IPR004738 Phosphate permease, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_004383-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_004428-T1 | IPR004695 Transporter protein SLAC1/Mae1/ Ssu1/TehA, IPR030185 Malic acid transport protein, IPR038665 Voltage-dependent anion channel superfamily | FALSE |
| XANPAGTX0501_004624-T1 | IPR004737 Nitrate transporter NarK/NarU-like, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_004972-T1 | IPR001905 Ammonium transporter, IPR018047 Ammonium transporter, conserved site, IPR024041 Ammonium transporter AmtB-like domain, IPR029020 Ammonium/urea transporter | FALSE |
| XANPAGTX0501_004996-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_005027-T1 | IPR003370 Chromate transporter, IPR014047 Chromate transporter, long chain | FALSE |
| XANPAGTX0501_005378-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_005489-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005571-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005572-T1 | IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005708-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006293-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006324-T1 | IPR001204 Phosphate transporter | FALSE |
| XANPAGTX0501_006367-T1 | IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006527-T1 | IPR000791 Acetate transporter GPR1/FUN34/SatP family | FALSE |
| XANPAGTX0501_007882-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_007969-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_008850-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR010929 CDR ABC transporter, IPR013525 ABC-2 type transporter, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR029481 ABC-transporter, N-terminal domain, IPR034001 ATP-binding cassette transporter, PDR-like subfamily G, domain 1, IPR034003 ATP-binding cassette transporter, PDR-like subfamily G, domain 2 | FALSE |
| XANPAGTX0501_009192-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009193-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009202-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009320-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009472-T1 | IPR005018 DOMON domain, IPR006593 Cytochrome b561/ferric reductase transmembrane, IPR015920 Cellobiose dehydrogenase, cytochrome domain, IPR018825 Domain of unknown function DUF2427, IPR036259 MFS transporter superfamily, IPR038697 None | FALSE |
| XANPAGTX0501_009914-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_010175-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010196-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010381-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_010444-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_010683-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010706-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR011527 ABC transporter type 1, transmembrane domain, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR036640 ABC transporter type 1, transmembrane domain superfamily | FALSE |
transport_cul<-funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("transport",InterPro_new),change=="culture") %>% select(TranscriptID,InterPro_new,lichen_ortho)
transport_lic %>%
kable(format = "html", col.names = c("TranscriptID","InterPro_new","lichen_ortho")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | InterPro_new | lichen_ortho |
|---|---|---|
| XANPAGTX0501_000142-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_000342-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_000342-T2 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_000684-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_000704-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_001082-T1 | IPR004853 Sugar phosphate transporter domain | FALSE |
| XANPAGTX0501_001448-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_001653-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_002486-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_003065-T3 | IPR005178 Organic solute transporter subunit alpha/Transmembrane protein 184 | FALSE |
| XANPAGTX0501_003337-T2 | IPR004738 Phosphate permease, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_004383-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_004428-T1 | IPR004695 Transporter protein SLAC1/Mae1/ Ssu1/TehA, IPR030185 Malic acid transport protein, IPR038665 Voltage-dependent anion channel superfamily | FALSE |
| XANPAGTX0501_004624-T1 | IPR004737 Nitrate transporter NarK/NarU-like, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_004972-T1 | IPR001905 Ammonium transporter, IPR018047 Ammonium transporter, conserved site, IPR024041 Ammonium transporter AmtB-like domain, IPR029020 Ammonium/urea transporter | FALSE |
| XANPAGTX0501_004996-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_005027-T1 | IPR003370 Chromate transporter, IPR014047 Chromate transporter, long chain | FALSE |
| XANPAGTX0501_005378-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_005489-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005571-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005572-T1 | IPR005828 Major facilitator, sugar transporter-like, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_005708-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006293-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006324-T1 | IPR001204 Phosphate transporter | FALSE |
| XANPAGTX0501_006367-T1 | IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_006527-T1 | IPR000791 Acetate transporter GPR1/FUN34/SatP family | FALSE |
| XANPAGTX0501_007882-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_007969-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_008850-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR010929 CDR ABC transporter, IPR013525 ABC-2 type transporter, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR029481 ABC-transporter, N-terminal domain, IPR034001 ATP-binding cassette transporter, PDR-like subfamily G, domain 1, IPR034003 ATP-binding cassette transporter, PDR-like subfamily G, domain 2 | FALSE |
| XANPAGTX0501_009192-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009193-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009202-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009320-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_009472-T1 | IPR005018 DOMON domain, IPR006593 Cytochrome b561/ferric reductase transmembrane, IPR015920 Cellobiose dehydrogenase, cytochrome domain, IPR018825 Domain of unknown function DUF2427, IPR036259 MFS transporter superfamily, IPR038697 None | FALSE |
| XANPAGTX0501_009914-T1 | IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_010175-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010196-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010381-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE |
| XANPAGTX0501_010444-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | TRUE |
| XANPAGTX0501_010683-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE |
| XANPAGTX0501_010706-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR011527 ABC transporter type 1, transmembrane domain, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR036640 ABC transporter type 1, transmembrane domain superfamily | FALSE |
secreted<-read.delim2("../../04_secretome/analysis_and_temp_files/01_predicting_effectors/all_secreted_list.txt",header=F)
secreted$TranscriptID<-str_replace(secreted$V1,"FUN","XANPAGTX0501")
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_secreted_all.png",res=300,width=2000,height=1500)
plot_transcript_heatmap(so, transcripts=secreted$TranscriptID,
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_secreted_all.png")
secreted_sig<-sig %>% filter(target_id %in% secreted$TranscriptID)
secreted_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 40
## 2 lichen 154
## 3 low_logFC 192
secreted<-read.delim2("../../04_secretome/analysis_and_temp_files/01_predicting_effectors/all_secreted_list.txt",header=F)
secreted$TranscriptID<-str_replace(secreted$V1,"FUN","XANPAGTX0501")
png("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_secreted_dge.png",res=300,width=2000,height=1500)
plot_transcript_heatmap(so, transcripts=secreted_sig$target_id[secreted_sig$change!="low_logFC"],
cluster_transcripts=T,show_rownames=F,
clustering_callback = callback)
dev.off()
## pdf
## 4
knitr::include_graphics("../analysis_and_temp_files/08_dge_culture_lichen/heatmap_secreted_dge.png")
secreted_table_lichen<-secreted_sig %>%
filter(change=="lichen") %>% left_join(funannot2,by = c("target_id"="TranscriptID")) %>% select(target_id,b,Product,CAZyme_new,COG_new,EggNog_new,GO.Terms_new,InterPro_new,PFAM_new,Protease_new,KO,lichen_ortho) %>%
arrange(b)
secreted_table_lichen %>%
kable(format = "html", col.names = colnames(secreted_table_lichen)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | Product | CAZyme_new | COG_new | EggNog_new | GO.Terms_new | InterPro_new | PFAM_new | Protease_new | KO | lichen_ortho |
|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_001127-T1 | -6.214566 | hypothetical protein | GH128 | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | PF11790 | NA | FALSE | |
| XANPAGTX0501_000655-T1 | -6.186697 | hypothetical protein | NA | NA | NA | NA | IPR035992 Ricin B-like lectins | NA | NA | FALSE | |
| XANPAGTX0501_009887-T1 | -6.152645 | hypothetical protein | NA | NA | ENOG503P63W | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_007865-T1 | -5.732812 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005533-T1 | -5.599048 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_010170-T1 | -5.061039 | hypothetical protein | NA | NA | NA | NA | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | NA | NA | TRUE | |
| XANPAGTX0501_001063-T1 | -4.589396 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009135-T1 | -4.527295 | hypothetical protein | NA | NA | NA | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_process: GO:0009405 - pathogenesis [Evidence IEA] | IPR011329 Killer toxin Kp4/SMK, IPR015131 Killer toxin, Kp4 | PF09044 | NA | FALSE | |
| XANPAGTX0501_005364-T1 | -4.400832 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_000656-T1 | -4.357565 | hypothetical protein | NA | NA | NA | NA | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | NA | NA | TRUE | |
| XANPAGTX0501_002409-T1 | -4.088717 | hypothetical protein | NA | NA | NA | GO_component: GO:0009277 - fungal-type cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | IPR001338 Hydrophobin | NA | NA | TRUE | |
| XANPAGTX0501_009189-T1 | -4.014594 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_001935-T1 | -3.959675 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006245-T1 | -3.929116 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_005061-T1 | -3.850853 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NVBA | NA | NA | PF13668 | NA | FALSE | |
| XANPAGTX0501_001856-T1 | -3.823871 | hypothetical protein | NA | NA | ENOG503P50I | NA | IPR037176 Osmotin/thaumatin-like superfamily | NA | NA | TRUE | |
| XANPAGTX0501_006282-T1 | -3.776836 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_004309-T1 | -3.720276 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_004881-T1 | -3.693406 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_001015-T1 | -3.506517 | hypothetical protein | NA | S:(S) Function unknown | ENOG503P58T, ENOG503P74E, ENOG503P76M | GO_process: GO:0042742 - defense response to bacterium [Evidence IEA], GO_process: GO:0050832 - defense response to fungus [Evidence IEA] | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | PF00967, PF03330 | NA | FALSE | |
| XANPAGTX0501_010044-T1 | -3.501860 | hypothetical protein | NA | Q:(Q) Secondary metabolites biosynthesis, transport and catabolism | ENOG503NTXA | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR002937 Amine oxidase, IPR036188 FAD/NAD(P)-binding domain superfamily | PF13450 | NA | FALSE | |
| XANPAGTX0501_009317-T1 | -3.484947 | hypothetical protein | NA | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily | NA | NA | FALSE | |
| XANPAGTX0501_009340-T1 | -3.459083 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006327-T1 | -3.436352 | hypothetical protein | NA | NA | NA | NA | IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal | PF10342 | NA | FALSE | |
| XANPAGTX0501_004930-T1 | -3.341143 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_002446-T1 | -3.286528 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_003765-T1 | -3.256318 | hypothetical protein | NA | NA | NA | GO_component: GO:0005618 - cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | IPR000420 Yeast PIR protein repeat | PF00399 | NA | FALSE | |
| XANPAGTX0501_005256-T1 | -3.224319 | hypothetical protein | AA7 | C:(C) Energy production and conversion | ENOG503NV4F | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565, PF08031 | NA | TRUE | |
| XANPAGTX0501_006846-T1 | -3.098928 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010449-T1 | -2.870515 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P0GD | GO_function: GO:0004222 - metalloendopeptidase activity [Evidence IEA], GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR001384 Peptidase M35, deuterolysin, IPR024079 Metallopeptidase, catalytic domain superfamily, IPR029463 Lysine-specific metallo-endopeptidase | PF02102, PF14521 | M35 | FALSE | |
| XANPAGTX0501_009688-T1 | -2.868656 | hypothetical protein | NA | NA | NA | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_function: GO:0030248 - cellulose binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000254 Cellulose-binding domain, fungal, IPR035971 Cellulose-binding domain superfamily, IPR036908 RlpA-like domain superfamily | PF00734 | NA | FALSE | |
| XANPAGTX0501_003270-T1 | -2.857225 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_004956-T1 | -2.837976 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005675-T1 | -2.825087 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NZAM | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | IPR008754 Peptidase M43, pregnancy-associated plasma-A, IPR024079 Metallopeptidase, catalytic domain superfamily | PF05572, PF13688 | M43B | FALSE | |
| XANPAGTX0501_000163-T1 | -2.730902 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NXZU | NA | IPR009078 Ferritin-like superfamily | PF13668 | NA | TRUE | |
| XANPAGTX0501_009886-T1 | -2.690801 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009668-T1 | -2.648950 | hypothetical protein | NA | NA | ENOG503P6EY | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_001304-T1 | -2.616995 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006142-T1 | -2.552912 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_003572-T1 | -2.535693 | hypothetical protein | CE16 | S:(S) Function unknown | ENOG503P02M | GO_function: GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA] | IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily | PF00657 | NA | FALSE | |
| XANPAGTX0501_009606-T1 | -2.529422 | hypothetical protein | NA | NA | ENOG503PMNB | NA | IPR011024 Gamma-crystallin-like | NA | NA | FALSE | |
| XANPAGTX0501_006291-T1 | -2.524612 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_008978-T1 | -2.518736 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005573-T1 | -2.506069 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_001458-T1 | -2.475919 | hypothetical protein | NA | G:(G) Carbohydrate transport and metabolism, O:(O) Posttranslational modification, protein turnover, chaperones, S:(S) Function unknown | ENOG503NVEA, ENOG503P073 | NA | IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 | PF01822, PF09362 | NA | FALSE | |
| XANPAGTX0501_005361-T1 | -2.474153 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_007976-T1 | -2.346686 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009683-T1 | -2.345949 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005733-T1 | -2.302949 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_010693-T1 | -2.297042 | hypothetical protein | AA7 | C:(C) Energy production and conversion | ENOG503NVX6 | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565 | NA | TRUE | |
| XANPAGTX0501_007272-T1 | -2.264531 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_002412-T1 | -2.245791 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010247-T1 | -2.240976 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_007515-T1 | -2.210135 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NUDE, ENOG503NV31 | GO_function: GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034163 Aspergillopepsin-like catalytic domain | PF00026 | A01A | FALSE | |
| XANPAGTX0501_005771-T1 | -2.208725 | hypothetical protein | GH5 | G:(G) Carbohydrate transport and metabolism | ENOG503NYXZ | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR001547 Glycoside hydrolase, family 5, IPR017853 Glycoside hydrolase superfamily | PF00150 | NA | FALSE | |
| XANPAGTX0501_007362-T1 | -2.200339 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010580-T1 | -2.189884 | hypothetical protein | NA | G:(G) Carbohydrate transport and metabolism | ENOG501RPBK | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR011048 Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR019405 Lactonase, 7-bladed beta propeller | PF10282 | NA | FALSE | |
| XANPAGTX0501_004978-T1 | -2.183515 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_001708-T1 | -2.176671 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_009730-T1 | -2.155593 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009615-T1 | -2.152340 | hypothetical protein | NA | NA | NA | NA | IPR035940 CAP superfamily | NA | NA | FALSE | |
| XANPAGTX0501_003873-T1 | -2.109258 | hypothetical protein | GH25 | G:(G) Carbohydrate transport and metabolism | ENOG503P1T2 | GO_function: GO:0003796 - lysozyme activity [Evidence IEA], GO_process: GO:0009253 - peptidoglycan catabolic process [Evidence IEA], GO_process: GO:0016998 - cell wall macromolecule catabolic process [Evidence IEA] | IPR002053 Glycoside hydrolase, family 25, IPR017853 Glycoside hydrolase superfamily, IPR018077 Glycoside hydrolase, family 25 subgroup | PF01183 | NA | FALSE | |
| XANPAGTX0501_004880-T1 | -2.100330 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_002331-T1 | -2.094181 | hypothetical protein | GH5 | G:(G) Carbohydrate transport and metabolism | ENOG503NY10 | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR001547 Glycoside hydrolase, family 5, IPR017853 Glycoside hydrolase superfamily, IPR018087 Glycoside hydrolase, family 5, conserved site | PF00150 | NA | FALSE | |
| XANPAGTX0501_007467-T1 | -2.047189 | hypothetical protein | CE3 | G:(G) Carbohydrate transport and metabolism, S:(S) Function unknown | ENOG503NXZG, ENOG503P4E6 | NA | IPR013830 SGNH hydrolase-type esterase domain, IPR036514 SGNH hydrolase superfamily | PF00657, PF13472, PF13517 | NA | FALSE | |
| XANPAGTX0501_008041-T1 | -2.018648 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010250-T1 | -1.956382 | hypothetical protein | NA | NA | ENOG503P3M4 | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_004329-T1 | -1.953200 | hypothetical protein | NA | NA | NA | NA | IPR020915 Uncharacterised protein family UPF0311 | PF11578 | NA | TRUE | |
| XANPAGTX0501_008875-T1 | -1.934027 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009699-T1 | -1.923092 | hypothetical protein | GH16 | G:(G) Carbohydrate transport and metabolism, O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NZM7, ENOG503PDKW | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_function: GO:0008061 - chitin binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily | PF00722 | NA | FALSE | |
| XANPAGTX0501_010470-T1 | -1.921148 | hypothetical protein | GH24 | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P2E0, ENOG503P2RE | GO_function: GO:0003796 - lysozyme activity [Evidence IEA], GO_process: GO:0009253 - peptidoglycan catabolic process [Evidence IEA], GO_process: GO:0016998 - cell wall macromolecule catabolic process [Evidence IEA], GO_process: GO:0019076 - viral release from host cell [Evidence IEA], GO_process: GO:0019835 - cytolysis [Evidence IEA] | IPR002196 Glycoside hydrolase, family 24, IPR009045 Hedgehog signalling/DD-peptidase zinc-binding domain superfamily, IPR023346 Lysozyme-like domain superfamily, IPR033907 Endolysin/autolysin, IPR034690 Endolysin T4 type | PF00959 | NA | K01185 | FALSE |
| XANPAGTX0501_000609-T1 | -1.909619 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_006349-T1 | -1.876403 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_000051-T1 | -1.859342 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_002665-T1 | -1.843112 | hypothetical protein | NA | NA | NA | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | IPR024079 Metallopeptidase, catalytic domain superfamily | NA | NA | TRUE | |
| XANPAGTX0501_001832-T1 | -1.829702 | hypothetical protein | GH128 | NA | NA | NA | IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | PF11790 | NA | TRUE | |
| XANPAGTX0501_004372-T1 | -1.826518 | hypothetical protein | NA | G:(G) Carbohydrate transport and metabolism, T:(T) Signal transduction mechanisms | ENOG503NV5A, ENOG503P0DZ | NA | IPR002018 Carboxylesterase, type B, IPR019819 Carboxylesterase type B, conserved site, IPR019826 Carboxylesterase type B, active site, IPR029058 Alpha/Beta hydrolase fold | PF00135, PF20434 | S09X | FALSE | |
| XANPAGTX0501_010022-T1 | -1.809156 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_000923-T1 | -1.786540 | hypothetical protein | NA | P:(P) Inorganic ion transport and metabolism | ENOG503NV06 | GO_function: GO:0003993 - acid phosphatase activity [Evidence IEA], GO_function: GO:0046872 - metal ion binding [Evidence IEA] | IPR008963 Purple acid phosphatase-like, N-terminal, IPR018946 PhoD-like phosphatase, metallophosphatase domain, IPR032093 Phospholipase D, N-terminal, IPR038607 PhoD-like superfamily | PF09423, PF16655 | NA | K01113 | FALSE |
| XANPAGTX0501_003361-T1 | -1.748190 | hypothetical protein | NA | NA | ENOG503P519 | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009511-T1 | -1.745629 | hypothetical protein | GH16 | G:(G) Carbohydrate transport and metabolism, O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NZM7, ENOG503PDKW | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_function: GO:0008061 - chitin binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily | PF00722 | NA | K01216 | FALSE |
| XANPAGTX0501_008019-T1 | -1.720017 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_002191-T1 | -1.708273 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006967-T1 | -1.686952 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_005715-T1 | -1.646345 | hypothetical protein | AA7 | C:(C) Energy production and conversion, O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NXN6, ENOG503P15H | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565, PF08031 | NA | FALSE | |
| XANPAGTX0501_006283-T1 | -1.624636 | hypothetical protein | NA | NA | NA | NA | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | NA | NA | TRUE | |
| XANPAGTX0501_008270-T1 | -1.619871 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005641-T1 | -1.614221 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_010366-T1 | -1.609971 | hypothetical protein | AA9 | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NYCR, ENOG503Q4YD | GO_function: GO:0003676 - nucleic acid binding [Evidence IEA], GO_function: GO:0008061 - chitin binding [Evidence IEA] | IPR001002 Chitin-binding, type 1, IPR005103 Auxiliary Activity family 9, IPR013087 Zinc finger C2H2-type, IPR018371 Chitin-binding, type 1, conserved site, IPR036861 Endochitinase-like superfamily | PF00187, PF03443 | NA | FALSE | |
| XANPAGTX0501_000467-T1 | -1.600285 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_008622-T1 | -1.585245 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_004346-T1 | -1.568986 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NUT8 | NA | IPR027589 Choice-of-anchor B domain | NA | NA | FALSE | |
| XANPAGTX0501_006257-T1 | -1.562667 | hypothetical protein | NA | G:(G) Carbohydrate transport and metabolism | ENOG503NW21 | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily | PF00332 | NA | K01210 | FALSE |
| XANPAGTX0501_007939-T1 | -1.548201 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_010021-T1 | -1.539151 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009026-T1 | -1.512207 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_003287-T1 | -1.493602 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_002186-T1 | -1.483447 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006194-T1 | -1.466337 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P7ES | NA | IPR036908 RlpA-like domain superfamily | NA | NA | TRUE | |
| XANPAGTX0501_004515-T1 | -1.449838 | hypothetical protein | NA | NA | NA | NA | IPR032710 NTF2-like domain superfamily, IPR037401 SnoaL-like domain | PF13577 | NA | FALSE | |
| XANPAGTX0501_010040-T1 | -1.448217 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010027-T1 | -1.444367 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_009972-T1 | -1.430084 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503Q3UA | GO_function: GO:0004252 - serine-type endopeptidase activity [Evidence IEA], GO_function: GO:0008236 - serine-type peptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR000209 Peptidase S8/S53 domain, IPR015366 Peptidase S53, activation domain, IPR030400 Sedolisin domain, IPR036852 Peptidase S8/S53 domain superfamily | PF00082, PF09286 | S53 | TRUE | |
| XANPAGTX0501_001919-T1 | -1.411388 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_000162-T1 | -1.389788 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_003766-T1 | -1.385254 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_003448-T1 | -1.383005 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_009936-T1 | -1.379267 | hypothetical protein | AA5, CBM32 | O:(O) Posttranslational modification, protein turnover, chaperones, S:(S) Function unknown | ENOG502I4WM, ENOG503NY8H | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR000421 Coagulation factor 5/8 C-terminal domain, IPR006652 Kelch repeat type 1, IPR008979 Galactose-binding-like domain superfamily, IPR011043 Galactose oxidase/kelch, beta-propeller, IPR013783 Immunoglobulin-like fold, IPR014756 Immunoglobulin E-set, IPR015202 Galactose oxidase-like, Early set domain, IPR037293 Galactose oxidase, central domain superfamily | PF00754, PF01344, PF09118 | NA | FALSE | |
| XANPAGTX0501_008146-T1 | -1.360688 | hypothetical protein | NA | E:(E) Amino acid transport and metabolism, O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P41K | GO_function: GO:0004185 - serine-type carboxypeptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR001563 Peptidase S10, serine carboxypeptidase, IPR018202 Serine carboxypeptidase, serine active site, IPR029058 Alpha/Beta hydrolase fold | PF00450 | S10 | K01288 | FALSE |
| XANPAGTX0501_010026-T1 | -1.349396 | hypothetical protein | NA | S:(S) Function unknown | ENOG503P0BZ | NA | IPR018392 LysM domain, IPR036779 LysM domain superfamily | PF01476 | NA | FALSE | |
| XANPAGTX0501_001455-T1 | -1.338580 | Sperm-associated antigen 4 protein | GH132 | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NUJ1 | NA | IPR005556 SUN family | PF03856 | NA | K01238 | FALSE |
| XANPAGTX0501_002315-T2 | -1.329521 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_009690-T1 | -1.325638 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_007280-T1 | -1.317948 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_004983-T1 | -1.308098 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005133-T1 | -1.291558 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NXPR | NA | IPR039535 Arylsulfotransferase-like | PF05935, PF14269 | NA | FALSE | |
| XANPAGTX0501_000606-T1 | -1.268241 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_007268-T1 | -1.263293 | hypothetical protein | AA7 | C:(C) Energy production and conversion, S:(S) Function unknown | ENOG503NXRX, ENOG503PBAU | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565, PF08031 | NA | TRUE | |
| XANPAGTX0501_004065-T1 | -1.250886 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006382-T1 | -1.241749 | hypothetical protein | NA | NA | ENOG503P53I | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005717-T1 | -1.235652 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_008990-T1 | -1.228845 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009689-T1 | -1.216985 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009731-T1 | -1.215351 | hypothetical protein | GH71 | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NVTC | GO_function: GO:0016787 - hydrolase activity [Evidence IEA] | IPR005197 Glycoside hydrolase family 71 | PF03659 | NA | K08254 | FALSE |
| XANPAGTX0501_008429-T1 | -1.195150 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_001183-T1 | -1.191723 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_000737-T1 | -1.183761 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010624-T1 | -1.176356 | hypothetical protein | NA | J:(J) Translation, ribosomal structure and biogenesis | ENOG503NVR9 | NA | IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | |
| XANPAGTX0501_003606-T1 | -1.168749 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005629-T1 | -1.163876 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NY4Y | GO_function: GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA], GO_process: GO:0006629 - lipid metabolic process [Evidence IEA] | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily, IPR030395 Glycerophosphodiester phosphodiesterase domain | PF03009 | NA | FALSE | |
| XANPAGTX0501_002565-T1 | -1.159972 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006751-T1 | -1.137824 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010682-T1 | -1.134135 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_000697-T1 | -1.131109 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_002041-T1 | -1.127546 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006292-T1 | -1.107115 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010443-T1 | -1.107115 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005317-T1 | -1.102348 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_002543-T1 | -1.098046 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006860-T1 | -1.097166 | hypothetical protein | NA | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily | NA | NA | FALSE | |
| XANPAGTX0501_007655-T1 | -1.094363 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NV1P | GO_function: GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA], GO_process: GO:0006629 - lipid metabolic process [Evidence IEA] | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily | NA | NA | FALSE | |
| XANPAGTX0501_001970-T1 | -1.089366 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009607-T1 | -1.069439 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_010370-T1 | -1.066233 | hypothetical protein | NA | NA | NA | NA | IPR003609 PAN/Apple domain | PF00024 | NA | FALSE | |
| XANPAGTX0501_002412-T2 | -1.065097 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_003285-T1 | -1.064411 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503NV2A | GO_function: GO:0008236 - serine-type peptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR008758 Peptidase S28, IPR029058 Alpha/Beta hydrolase fold, IPR042269 Serine carboxypeptidase S28, SKS domain | NA | S28 | K09649 | FALSE |
| XANPAGTX0501_000434-T1 | -1.045784 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_003186-T1 | -1.045733 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009011-T1 | -1.036787 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_002514-T1 | -1.030316 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_008683-T1 | -1.021294 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009311-T1 | -1.019264 | hypothetical protein | NA | NA | NA | NA | IPR008427 Extracellular membrane protein, CFEM domain | PF05730 | NA | TRUE | |
| XANPAGTX0501_008027-T1 | -1.017996 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NZ6V | GO_function: GO:0004601 - peroxidase activity [Evidence IEA] | IPR000028 Chloroperoxidase, IPR036851 Chloroperoxidase-like superfamily | PF01328 | NA | FALSE | |
| XANPAGTX0501_003124-T1 | -1.008637 | hypothetical protein | NA | O:(O) Posttranslational modification, protein turnover, chaperones | ENOG503P2G1 | GO_function: GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA], GO_process: GO:0006508 - proteolysis [Evidence IEA] | IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034164 Pepsin-like domain | PF00026 | A01A | FALSE |
secreted_table_culture<-secreted_sig %>%
filter(change=="culture") %>% left_join(funannot2,by = c("target_id"="TranscriptID")) %>% select(target_id,b,Product,CAZyme_new,COG_new,EggNog_new,GO.Terms_new,InterPro_new,PFAM_new,Protease_new,KO,lichen_ortho) %>%
arrange(desc(b))
secreted_table_culture %>%
kable(format = "html", col.names = colnames(secreted_table_culture)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | Product | CAZyme_new | COG_new | EggNog_new | GO.Terms_new | InterPro_new | PFAM_new | Protease_new | KO | lichen_ortho |
|---|---|---|---|---|---|---|---|---|---|---|---|
| XANPAGTX0501_005691-T1 | 5.859572 | hypothetical protein | AA7 | C:(C) Energy production and conversion | ENOG503NVX6 | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565 | NA | TRUE | |
| XANPAGTX0501_005118-T1 | 5.651733 | hypothetical protein | NA | NA | ENOG503PWV2, ENOG503PYSR | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_006848-T1 | 3.980717 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_008294-T1 | 3.732327 | hypothetical protein | AA5, CBM32 | O:(O) Posttranslational modification, protein turnover, chaperones, S:(S) Function unknown | ENOG502I4WM, ENOG503NY8H | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR000421 Coagulation factor 5/8 C-terminal domain, IPR006652 Kelch repeat type 1, IPR008979 Galactose-binding-like domain superfamily, IPR011043 Galactose oxidase/kelch, beta-propeller, IPR013783 Immunoglobulin-like fold, IPR014756 Immunoglobulin E-set, IPR015202 Galactose oxidase-like, Early set domain, IPR037293 Galactose oxidase, central domain superfamily | PF00754, PF01344, PF09118 | NA | FALSE | |
| XANPAGTX0501_010474-T1 | 3.724444 | hypothetical protein | NA | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily | NA | NA | FALSE | |
| XANPAGTX0501_003863-T2 | 3.301034 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_000306-T1 | 3.231592 | hypothetical protein | NA | S:(S) Function unknown | ENOG503P21A | NA | IPR021851 Protein of unknown function DUF3455 | PF11937 | NA | FALSE | |
| XANPAGTX0501_006869-T1 | 3.075100 | hypothetical protein | GH128 | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | PF11790 | NA | FALSE | |
| XANPAGTX0501_005759-T1 | 2.880832 | hypothetical protein | NA | NA | ENOG503P558 | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009761-T1 | 2.701300 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NZQD | GO_component: GO:0005576 - extracellular region [Evidence IEA] | IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR034120 None, IPR035940 CAP superfamily | PF00188 | NA | K20412 | FALSE |
| XANPAGTX0501_000850-T1 | 2.534878 | hypothetical protein | NA | NA | ENOG503P7C3 | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_006926-T1 | 2.528494 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | TRUE | |
| XANPAGTX0501_009613-T1 | 2.515673 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NZZ0 | NA | IPR000073 Alpha/beta hydrolase fold-1, IPR029058 Alpha/Beta hydrolase fold | PF12697 | NA | TRUE | |
| XANPAGTX0501_010126-T2 | 2.407552 | hypothetical protein | NA | NA | NA | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | IPR024079 Metallopeptidase, catalytic domain superfamily | NA | NA | FALSE | |
| XANPAGTX0501_009170-T1 | 2.253664 | hypothetical protein | GH45 | G:(G) Carbohydrate transport and metabolism | ENOG503P08U, ENOG503Q3X3 | GO_function: GO:0008810 - cellulase activity [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR000334 Glycoside hydrolase, family 45, IPR036908 RlpA-like domain superfamily | PF02015 | NA | FALSE | |
| XANPAGTX0501_001974-T1 | 2.218747 | hypothetical protein | AA7 | C:(C) Energy production and conversion | ENOG503NWXH | GO_function: GO:0016491 - oxidoreductase activity [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_function: GO:0071949 - FAD binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | PF01565, PF08031 | NA | TRUE | |
| XANPAGTX0501_010307-T1 | 1.956031 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_003850-T1 | 1.889111 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009609-T1 | 1.620965 | hypothetical protein | NA | I:(I) Lipid transport and metabolism, S:(S) Function unknown | ENOG503NZ1V | GO_function: GO:0004806 - triglyceride lipase activity [Evidence IEA], GO_process: GO:0016042 - lipid catabolic process [Evidence IEA] | IPR000073 Alpha/beta hydrolase fold-1, IPR005152 Lipase, secreted, IPR022742 Serine aminopeptidase, S33, IPR029058 Alpha/Beta hydrolase fold | PF03583, PF12146, PF12697 | NA | TRUE | |
| XANPAGTX0501_010442-T1 | 1.618450 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_005664-T1 | 1.551288 | hypothetical protein | GH128 | NA | NA | NA | IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | PF11790 | NA | FALSE | |
| XANPAGTX0501_007937-T1 | 1.503271 | hypothetical protein | NA | NA | ENOG503NVDR | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR011044 Quinoprotein amine dehydrogenase, beta chain-like, IPR015943 WD40/YVTN repeat-like-containing domain superfamily | NA | NA | FALSE | |
| XANPAGTX0501_000401-T1 | 1.401801 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_007985-T1 | 1.397612 | hypothetical protein | NA | NA | NA | GO_function: GO:0008237 - metallopeptidase activity [Evidence IEA] | IPR024079 Metallopeptidase, catalytic domain superfamily | NA | NA | FALSE | |
| XANPAGTX0501_006091-T1 | 1.369228 | hypothetical protein | NA | NA | ENOG503P8K1 | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_009962-T1 | 1.333092 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_007182-T1 | 1.319524 | alpha,alpha-trehalase ath1 | NA | G:(G) Carbohydrate transport and metabolism | ENOG503NUMQ | GO_function: GO:0003824 - catalytic activity [Evidence IEA], GO_function: GO:0030246 - carbohydrate binding [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR005195 Glycoside hydrolase, family 65, central catalytic, IPR005196 Glycoside hydrolase, family 65, N-terminal, IPR008928 Six-hairpin glycosidase superfamily, IPR008979 Galactose-binding-like domain superfamily, IPR011013 Galactose mutarotase-like domain superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR037018 Glycoside hydrolase family 65, N-terminal domain superfamily | PF03633, PF03636 | NA | FALSE | |
| XANPAGTX0501_010132-T1 | 1.308632 | hypothetical protein | GH43 | G:(G) Carbohydrate transport and metabolism | ENOG503P1F3 | GO_function: GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA], GO_process: GO:0005975 - carbohydrate metabolic process [Evidence IEA] | IPR006710 Glycoside hydrolase, family 43, IPR023296 Glycosyl hydrolase, five-bladed beta-propellor domain superfamily | PF04616 | NA | FALSE | |
| XANPAGTX0501_005244-T1 | 1.304550 | hypothetical protein | AA3 | E:(E) Amino acid transport and metabolism | ENOG503NU6B, ENOG503NUFD | GO_function: GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | PF00732, PF05199 | NA | K00115 | FALSE |
| XANPAGTX0501_007388-T1 | 1.269375 | hypothetical protein | NA | S:(S) Function unknown | ENOG503P3AN | GO_function: GO:0005515 - protein binding [Evidence IEA] | IPR002372 Pyrrolo-quinoline quinone repeat, IPR011047 Quinoprotein alcohol dehydrogenase-like superfamily, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat | NA | NA | FALSE | |
| XANPAGTX0501_006386-T1 | 1.206100 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_002723-T1 | 1.203666 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NXPR | NA | IPR039535 Arylsulfotransferase-like | PF05935, PF14269 | NA | FALSE | |
| XANPAGTX0501_006694-T1 | 1.155895 | hypothetical protein | NA | NA | ENOG503P24M | NA | NA | NA | NA | FALSE | |
| XANPAGTX0501_010191-T1 | 1.151281 | hypothetical protein | CE5 | G:(G) Carbohydrate transport and metabolism | ENOG503P4Q7 | GO_component: GO:0005576 - extracellular region [Evidence IEA], GO_function: GO:0016787 - hydrolase activity [Evidence IEA], GO_function: GO:0050525 - cutinase activity [Evidence IEA] | IPR000675 Cutinase/acetylxylan esterase, IPR011150 Cutinase, monofunctional, IPR029058 Alpha/Beta hydrolase fold | PF01083 | NA | FALSE | |
| XANPAGTX0501_001051-T1 | 1.077085 | hypothetical protein | GH17 | G:(G) Carbohydrate transport and metabolism | ENOG503NXKT | NA | IPR017853 Glycoside hydrolase superfamily | NA | NA | FALSE | |
| XANPAGTX0501_009124-T1 | 1.069091 | hypothetical protein | NA | S:(S) Function unknown | ENOG503NVXI, ENOG503P4UQ | GO_component: GO:0005618 - cell wall [Evidence IEA], GO_function: GO:0005199 - structural constituent of cell wall [Evidence IEA] | IPR000420 Yeast PIR protein repeat | PF00399 | NA | FALSE | |
| XANPAGTX0501_007482-T1 | 1.051174 | hypothetical protein | GH132 | S:(S) Function unknown | ENOG503NVKV | NA | IPR005556 SUN family | PF03856 | NA | FALSE | |
| XANPAGTX0501_003140-T1 | 1.035102 | hypothetical protein | AA3 | E:(E) Amino acid transport and metabolism | ENOG503PBWU | GO_function: GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA], GO_function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA], GO_process: GO:0055114 - oxidation-reduction process [Evidence IEA] | IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | PF00732, PF05199 | NA | TRUE | |
| XANPAGTX0501_009902-T1 | 1.034038 | hypothetical protein | NA | P:(P) Inorganic ion transport and metabolism | ENOG503NY8E | NA | IPR001148 Alpha carbonic anhydrase domain, IPR036398 Alpha carbonic anhydrase domain superfamily, IPR041891 Carbonic anhydrase, prokaryotic-like | PF00194 | NA | K01672 | FALSE |
| XANPAGTX0501_010393-T1 | 1.019087 | hypothetical protein | NA | NA | NA | NA | NA | NA | NA | FALSE |
nlr_list<-read.delim2("../../02_mycobiont_genome/analysis_and_temp_files/10_nlr/NLRs.txt")
nlr_sig<-sig %>% filter(target_id %in% nlr_list$TranscriptID)
nlr_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 1
## 2 lichen 4
## 3 low_logFC 9
nlr_lichen<-nlr_sig$target_id[nlr_sig$change=="lichen"]
plot_bootstrap(so,
target_id = nlr_lichen[1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlr_lichen[2],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlr_lichen[3],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlr_lichen[4],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlr_sig$target_id[nlr_sig$change=="culture"],
units = "est_counts",
color_by = "condition")
nlr_like<-read.delim2("../../02_mycobiont_genome/analysis_and_temp_files/10_nlr/NLR_like.txt")
nlrlike_sig<-sig %>% filter(target_id %in% nlr_like$TranscriptID) %>% arrange(b)
nlrlike_sig %>% group_by(change) %>% summarise(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 3
## 2 lichen 12
## 3 low_logFC 14
plot_bootstrap(so,
target_id = nlrlike_sig$target_id[1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlrlike_sig$target_id[2],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = nlrlike_sig$target_id[3],
units = "est_counts",
color_by = "condition")
funannot2 %>% filter(grepl("IPR038305",InterPro_new) |
grepl("IPR029498",InterPro_new) |
grepl("IPR010730",InterPro_new)) %>%
group_by(lichen_ortho) %>% summarize(n=n())
## # A tibble: 2 × 2
## lichen_ortho n
## <lgl> <int>
## 1 FALSE 57
## 2 TRUE 16
het_sig<-funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR038305",InterPro_new) |
grepl("IPR029498",InterPro_new) |
grepl("IPR010730",InterPro_new)) %>% arrange(b)
het_sig %>% group_by(change) %>% summarize(n=n())
## # A tibble: 4 × 2
## change n
## <chr> <int>
## 1 culture 6
## 2 lichen 14
## 3 low_logFC 24
## 4 <NA> 29
het_sig2<-het_sig %>% filter(!(TranscriptID %in% nlrlike_sig$target_id),!is.na(b))
het_sig2 %>% group_by(change) %>% summarize(n=n())
## # A tibble: 3 × 2
## change n
## <chr> <int>
## 1 culture 5
## 2 lichen 10
## 3 low_logFC 20
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[2],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[3],
units = "est_counts",
color_by = "condition")
* Visualize most culture-upregulated * For first and third, expression in lichens is very non-uniform * Second looks more regular
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[nrow(het_sig2)],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[nrow(het_sig2)-1],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = het_sig2$TranscriptID[nrow(het_sig2)-2],
units = "est_counts",
color_by = "condition")
fbox<-sig2 %>% filter(grepl("F-box",InterPro_new),change!="low_logFC")
plot_bootstrap(so,
target_id = fbox$target_id[10],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = fbox$target_id[9],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = fbox$target_id[4],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = fbox$target_id[5],
units = "est_counts",
color_by = "condition")
poz<-sig2 %>% filter(grepl("BTB/POZ",InterPro_new),change!="low_logFC")
plot_bootstrap(so,
target_id = poz$target_id[3],
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_002123-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_003775-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_008184-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_001825-T1",
units = "est_counts",
color_by = "condition")
plot_bootstrap(so,
target_id = "XANPAGTX0501_009737-T1",
units = "est_counts",
color_by = "condition")
mult_gene_table %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(Function=="Transcription factors") %>%
group_by(change,Description) %>% summarize(n=n()) %>%
pivot_wider(names_from = change,values_from = n,values_fill=0) %>%
filter(culture!=0 | lichen!=0)
## `summarise()` has grouped output by 'change'. You can override using the
## `.groups` argument.
## # A tibble: 9 × 5
## Description culture lichen low_logFC `NA`
## <chr> <int> <int> <int> <int>
## 1 Basic-leucine zipper domain 1 0 10 7
## 2 DNA binding HTH domain, Psq-type 1 0 0 0
## 3 Fungal transcription factor 3 1 7 9
## 4 Helix-loop-helix DNA-binding domain superfamily 1 0 0 6
## 5 Zinc finger C2H2-type 1 9 36 41
## 6 Zinc finger, RING/FYVE/PHD-type 1 4 41 60
## 7 Zn(2)-C6 fungal-type DNA-binding domain superf… 9 6 37 37
## 8 Homeobox domain 0 1 4 0
## 9 Transcription factor domain, fungi 0 2 21 21
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR013087",InterPro),change %in% c("lichen","culture")) %>%
select(TranscriptID,b,change,Product,InterPro) %>%
kable(format = "html", col.names = c("TranscriptID","b","change","product","InterPro")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | b | change | product | InterPro |
|---|---|---|---|---|
| XANPAGTX0501_000420-T1 | -1.619168 | lichen | hypothetical protein | IPR013087 Zinc finger C2H2-type |
| XANPAGTX0501_000984-T1 | -3.164451 | lichen | hypothetical protein | IPR002151 Kinesin light chain;IPR011990 Tetratricopeptide-like helical domain superfamily;IPR013026 None;IPR013087 Zinc finger C2H2-type;IPR019734 Tetratricopeptide repeat |
| XANPAGTX0501_001247-T1 | -2.397327 | lichen | hypothetical protein | IPR013087 Zinc finger C2H2-type;IPR036236 Zinc finger C2H2 superfamily |
| XANPAGTX0501_001515-T1 | -1.263312 | lichen | hypothetical protein | IPR013087 Zinc finger C2H2-type |
| XANPAGTX0501_006931-T1 | -1.314529 | lichen | hypothetical protein | IPR013087 Zinc finger C2H2-type |
| XANPAGTX0501_007754-T1 | -2.683149 | lichen | hypothetical protein | IPR013087 Zinc finger C2H2-type;IPR019447 DNA/RNA-binding protein Kin17, WH-like domain;IPR036236 Zinc finger C2H2 superfamily;IPR038254 DNA/RNA-binding protein KIN17, WH-like domain superfamily |
t<-mult_gene_table %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(Function=="Transcription factors") %>%
group_by(change,Description) %>% summarize(n=n()) %>%
pivot_wider(names_from = change,values_from = n,values_fill=0)
## `summarise()` has grouped output by 'change'. You can override using the
## `.groups` argument.
colnames(t)<-c("Description","culture","lichen","low_logFC","Non")
t %>% mutate(sum=culture+lichen+low_logFC+Non) %>%arrange(desc(sum)) %>%
kable(format = "html", col.names = c("Description","culture","lichen","low_logFC","Non","sum")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| Description | culture | lichen | low_logFC | Non | sum |
|---|---|---|---|---|---|
| Zinc finger, RING/FYVE/PHD-type | 1 | 4 | 41 | 60 | 106 |
| Zn(2)-C6 fungal-type DNA-binding domain superfamily | 9 | 6 | 37 | 37 | 89 |
| Zinc finger C2H2-type | 1 | 9 | 36 | 41 | 87 |
| Transcription factor domain, fungi | 0 | 2 | 21 | 21 | 44 |
| Fungal transcription factor | 3 | 1 | 7 | 9 | 20 |
| Basic-leucine zipper domain | 1 | 0 | 10 | 7 | 18 |
| Fork head domain | 0 | 0 | 5 | 4 | 9 |
| Myb domain | 0 | 0 | 4 | 4 | 8 |
| Helix-loop-helix DNA-binding domain superfamily | 1 | 0 | 0 | 6 | 7 |
| Zinc finger, GATA-type | 0 | 0 | 3 | 4 | 7 |
| Transcription factor CBF/NF-Y/archaeal histone domain | 0 | 0 | 3 | 3 | 6 |
| Homeobox domain | 0 | 1 | 4 | 0 | 5 |
| HTH APSES-type DNA-binding domain superfamily | 0 | 0 | 2 | 3 | 5 |
| Zinc finger, TFIIS-type | 0 | 0 | 1 | 4 | 5 |
| Heat shock factor (HSF)-type, DNA-binding | 0 | 0 | 1 | 2 | 3 |
| Zinc finger, MIZ-type | 0 | 0 | 1 | 2 | 3 |
| Zinc finger, NF-X1-type | 0 | 0 | 3 | 0 | 3 |
| Nuclear transcription factor Y subunit A | 0 | 0 | 2 | 0 | 2 |
| PAS fold | 0 | 0 | 1 | 1 | 2 |
| Transcription Factor IIF, Rap30/Rap74, interaction | 0 | 0 | 1 | 1 | 2 |
| Transcription factor TFIIB | 0 | 0 | 1 | 1 | 2 |
| Transcription factor, MADS-box | 0 | 0 | 2 | 0 | 2 |
| p53-like transcription factor, DNA-binding domain superfamily | 0 | 0 | 1 | 1 | 2 |
| DNA-binding RFX-type winged-helix domain | 0 | 0 | 0 | 2 | 2 |
| Transcription factor IIIC subunit 5, HTH domain | 0 | 0 | 0 | 2 | 2 |
| Transcription factor IIS, N-termina | 0 | 0 | 0 | 2 | 2 |
| DNA binding HTH domain, Psq-type | 1 | 0 | 0 | 0 | 1 |
| CP2 transcription factor | 0 | 0 | 1 | 0 | 1 |
| NDT80 DNA-binding domain superfamily | 0 | 0 | 1 | 0 | 1 |
| SNU66/SART1 family | 0 | 0 | 1 | 0 | 1 |
| TFIIH C1-like domain | 0 | 0 | 1 | 0 | 1 |
| Transcription factor IIIC, 90kDa subunit, N-terminal | 0 | 0 | 1 | 0 | 1 |
| Transcription factor Opi1 | 0 | 0 | 1 | 0 | 1 |
| Transcription factor TFIIIB component B, Myb domain | 0 | 0 | 1 | 0 | 1 |
| Transcription factor, NFYB/HAP3, conserved site | 0 | 0 | 1 | 0 | 1 |
| Transcription initiation factor IIA, gamma subunit | 0 | 0 | 1 | 0 | 1 |
| Zinc finger, BED-type | 0 | 0 | 1 | 0 | 1 |
| Zinc finger, C5HC2-type | 0 | 0 | 1 | 0 | 1 |
| Zinc finger, GRF-type | 0 | 0 | 1 | 0 | 1 |
| Apoptosis-antagonizing transcription factor, C-terminal | 0 | 0 | 0 | 1 | 1 |
| CCR4-Not complex component, Not1, C-terminal | 0 | 0 | 0 | 1 | 1 |
| DDT domain | 0 | 0 | 0 | 1 | 1 |
| General transcription factor TFIIH, subunit Tfb6 | 0 | 0 | 0 | 1 | 1 |
| TEA/ATTS domain | 0 | 0 | 0 | 1 | 1 |
| Transcription factor IIA, alpha/beta subunit | 0 | 0 | 0 | 1 | 1 |
| Transcription factor Nrm1/Whi5 | 0 | 0 | 0 | 1 | 1 |
| Transcription factor Spt20 | 0 | 0 | 0 | 1 | 1 |
| Transcription factor Ste12 | 0 | 0 | 0 | 1 | 1 |
| Transcription factor TFIID, subunit 8, C-terminal | 0 | 0 | 0 | 1 | 1 |
| Transcription factor TFIIE beta subunit, DNA-binding domain | 0 | 0 | 0 | 1 | 1 |
| Transcription factor TFIIH subunit p52/Tfb2 | 0 | 0 | 0 | 1 | 1 |
| Transcription factor TFIIIC, triple barrel domain | 0 | 0 | 0 | 1 | 1 |
| Transcription factor, Skn7-like | 0 | 0 | 0 | 1 | 1 |
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR013083",InterPro),change %in% c("lichen","culture")) %>%
select(TranscriptID,b,change,Product,InterPro) %>%
kable(format = "html", col.names = c("TranscriptID","b","change","product","InterPro")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | b | change | product | InterPro |
|---|---|---|---|---|
| XANPAGTX0501_002947-T1 | -1.534891 | lichen | hypothetical protein | IPR000330 SNF2, N-terminal;IPR001650 Helicase, C-terminal;IPR001841 Zinc finger, RING-type;IPR013083 Zinc finger, RING/FYVE/PHD-type;IPR014001 Helicase superfamily 1/2, ATP-binding domain;IPR017907 Zinc finger, RING-type, conserved site;IPR018957 Zinc finger, C3HC4 RING-type;IPR027417 P-loop containing nucleoside triphosphate hydrolase;IPR038718 SNF2-like, N-terminal domain superfamily |
| XANPAGTX0501_005479-T1 | 2.092073 | culture | peroxisome bioproteinsis factor 10 | IPR001841 Zinc finger, RING-type;IPR006845 Pex, N-terminal;IPR013083 Zinc finger, RING/FYVE/PHD-type;IPR017907 Zinc finger, RING-type, conserved site |
| XANPAGTX0501_006448-T1 | -1.199765 | lichen | hypothetical protein | IPR001841 Zinc finger, RING-type;IPR013083 Zinc finger, RING/FYVE/PHD-type |
| XANPAGTX0501_009436-T1 | -1.317000 | lichen | hypothetical protein | IPR000330 SNF2, N-terminal;IPR001650 Helicase, C-terminal;IPR001841 Zinc finger, RING-type;IPR013083 Zinc finger, RING/FYVE/PHD-type;IPR014001 Helicase superfamily 1/2, ATP-binding domain;IPR027417 P-loop containing nucleoside triphosphate hydrolase;IPR038718 SNF2-like, N-terminal domain superfamily |
funannot2 %>% left_join(sig,by=c("TranscriptID"="target_id")) %>%
filter(grepl("IPR036864",InterPro),change %in% c("lichen","culture")) %>%
select(TranscriptID,b,change,Product,InterPro) %>%
kable(format = "html", col.names = c("TranscriptID","b","change","product","InterPro")) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | b | change | product | InterPro |
|---|---|---|---|---|
| XANPAGTX0501_001980-T1 | 1.496530 | culture | hypothetical protein | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain;IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily |
| XANPAGTX0501_002161-T1 | 2.266902 | culture | hypothetical protein | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain;IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily |
| XANPAGTX0501_002427-T1 | -1.786972 | lichen | hypothetical protein | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain;IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily |
| XANPAGTX0501_002762-T1 | 1.105893 | culture | DNA-binding transcriptional regulator ume6 | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain;IPR021858 Fungal transcription factor;IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily |
| XANPAGTX0501_004715-T1 | -1.034993 | lichen | Transcriptional regulator of nonfermentable carbon utilization | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain;IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily |
| XANPAGTX0501_005120-T1 | 5.474386 | culture | hypothetical protein | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain;IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily |
| XANPAGTX0501_005608-T1 | 2.365288 | culture | hypothetical protein | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain;IPR021858 Fungal transcription factor;IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily |
| XANPAGTX0501_009300-T1 | 1.743077 | culture | hypothetical protein | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain;IPR021858 Fungal transcription factor;IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily |
#make color mapping consistent between different heatmaps
library(circlize)
library(extrafont)
col_fun <- colorRamp2(seq(0,8,length.out = 100), viridis(100))
filt_mat<-subset(trans_mat, rownames(trans_mat) %in% annotation$TranscriptID)
HM_all = Heatmap(filt_mat, show_row_names = F, show_column_names = T, row_title_rot = 0, col=col_fun,top_annotation = ta,heatmap_legend_param = list(title = "Expression: log(TPM)"))
#get the column order
colord<-column_order(HM_all)
## Warning: The heatmap has not been initialized. You might have different results
## if you repeatedly execute this function, e.g. when row_km/column_km was
## set. It is more suggested to do as `ht = draw(ht); column_order(ht)`.
colord<-colnames(filt_mat)[colord]
draw(HM_all)
pdf(file="../results/big_heatmap_unseparated.pdf",width=6,height=6)
draw(HM_all)
dev.off()
## quartz_off_screen
## 2
#define function
draw_heatmap_by_group<-function(gene_group,annotation_table = annotation_temp,matrix = trans_mat, order = colord){
list<-annotation_table$TranscriptID[annotation_table$Function==gene_group]
filt_mat<-subset(matrix, rownames(matrix) %in% list)
HM = Heatmap(filt_mat, show_row_names = F, show_column_names = T, row_title = gene_group, row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = order,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
return(HM)
}
#make a list of all gene groups in the right order
annotation_temp<-annotation %>% left_join(mult_list %>% select(Function, Function_type) %>% unique()) %>% arrange(Function)
annotation_temp$Function_type<-factor(annotation_temp$Function_type,
levels=c("Fungal multicellularity", "Expression regulation","Signal transduction"),ordered = T)
annotation_temp<-annotation_temp %>% arrange(Function_type)
#rename some of the functions to make shorter
annotation_temp$Function[annotation_temp$Function=="Acetyl-CoA production and metabolism"]<-"Acetyl-CoA production\nand metabolism"
annotation_temp$Function[annotation_temp$Function=="Cell division, proliferation and growth"]<-"Cell division and growth"
annotation_temp$Function[annotation_temp$Function=="Cell surface and cell wall proteins"]<-"Cell wall proteins"
annotation_temp$Function[annotation_temp$Function=="Cell surface and cell wall proteins"]<-"Cell wall proteins"
#apply to all gene groups
l<-lapply(as.vector(unique(annotation_temp$Function)),draw_heatmap_by_group)
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#add other gene groups, which aren't in the multicellularity list
#protein kinases
kinase_list<-funannot$TranscriptID[grepl("IPR000719",funannot$InterPro_new) & funannot$TranscriptID %in% sig$target_id[sig$change %in% c("lichen","culture")]]
filt_mat_kinase<-subset(trans_mat, rownames(trans_mat) %in% kinase_list)
HM_kinase = Heatmap(filt_mat_kinase, show_row_names = F, show_column_names = T, row_title = "Protein Kinases", row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#NLRs
nlr_list<-nlr_sig$target_id[nlr_sig$change %in% c("lichen","culture")]
filt_mat_nlr<-subset(trans_mat, rownames(trans_mat) %in% nlr_list)
HM_nlr = Heatmap(filt_mat_nlr, show_row_names = F, show_column_names = T, row_title = "Putative NLRs", row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#Other het-incopatibility
het_list<-het_sig$TranscriptID[het_sig$change %in% c("lichen","culture") & !(het_sig$TranscriptID %in% nlr_list)]
filt_mat_het<-subset(trans_mat, rownames(trans_mat) %in% het_list)
HM_het = Heatmap(filt_mat_het, show_row_names = F, show_column_names = T, row_title = "Other self/non-self\nrecognition", row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#replace 4 panels for signaling pathways with one
signaling_list<-annotation$TranscriptID[annotation$Function %in% c("G-proteins and GPCR", "MAPK signaling pathway","Oxylipins","Velvet")]
filt_mat_signal<-subset(trans_mat, rownames(trans_mat) %in% signaling_list)
HM_signal = Heatmap(filt_mat_signal, show_row_names = F, show_column_names = T, row_title = "Signal transduction", row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"))
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
#draw
ht_list <- l[[4]] %v% l[[5]] %v% l[[7]] %v% l[[6]] %v% l[[3]] %v% l[[8]] %v%
l[[20]] %v% l[[14]] %v% l[[1]] %v% l[[11]] %v% l[[2]] %v% l[[15]] %v% l[[16]] %v% l[[19]] %v% HM_signal %v% HM_kinase %v% HM_nlr %v% HM_het
#draw in two parts
ht_list1 <- l[[4]] %v% l[[5]] %v% l[[7]] %v% l[[6]] %v% l[[3]] %v% l[[8]] %v%
l[[20]] %v% l[[14]] %v% l[[1]] %v% l[[11]] %v% l[[2]]
ht_list2 <- l[[15]] %v% l[[16]] %v% l[[19]] %v% HM_signal %v% HM_kinase %v% HM_nlr %v% HM_het
draw(ht_list1)
pdf(file="../results/big_heatmap_part1.pdf",width=4.25,height=4.5)
draw(ht_list1, newpage = FALSE)
dev.off()
## quartz_off_screen
## 2
pdf(file="../results/big_heatmap_part2.pdf",width=4,height=3.5)
draw(ht_list2)
dev.off()
## quartz_off_screen
## 2
parietin_list<-c("XANPAGTX0501_008850-T1","XANPAGTX0501_008851-T1","XANPAGTX0501_008852-T1","XANPAGTX0501_008853-T1")
filt_mat_parietin<-subset(trans_mat, rownames(trans_mat) %in% parietin_list)
HM_parietin = Heatmap(filt_mat_parietin, show_row_names = T, show_column_names = T,cluster_rows = FALSE, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta)
pdf(file="../results/parietin_heatmap.pdf",width=10,height=2.5)
draw(HM_parietin)
dev.off()
## quartz_off_screen
## 2
HM_parietin
secreted_list<-secreted_sig$target_id[secreted_sig$change!="low_logFC"]
filt_mat_secreted<-subset(trans_mat, rownames(trans_mat) %in% secreted_list)
HM_secreted = Heatmap(filt_mat_secreted, show_row_names = F, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta)
pdf(file="../results/secreted_dge_heatmap.pdf",width=10,height=8)
draw(HM_secreted)
dev.off()
## quartz_off_screen
## 2
HM_secreted
plot_bootstrap(so,
target_id = "XANPAGTX0501_009887-T1",
units = "est_counts",
color_by = "condition")
* Make heat map for the same effector
filt_mat_eff<-subset(trans_mat, rownames(trans_mat) =="XANPAGTX0501_009887-T1")
HM_eff = Heatmap(filt_mat_eff, show_row_names = F, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta)
pdf(file="../results/XANPAGTX0501_009887-T1_heatmap.pdf",width=10,height=2)
draw(HM_eff)
dev.off()
## quartz_off_screen
## 2
HM_eff
antismash_core<-antismash_gene_all %>% filter(Core_gene==T) %>%
left_join(funannot2,relationship = "many-to-many") %>%
left_join(sig, by = c("TranscriptID"="target_id"))
filt_mat_core<-subset(trans_mat, rownames(trans_mat) %in% antismash_core$TranscriptID)
#define row annotation
##for one protein, XANPAGTX0501_001694-T1, we had two annotations since it is a core gene in two cluster: Xp_GTX0501_2_Cluster_6 and Xp_GTX0501_2_Cluster_7. here I picked Xp_GTX0501_2_Cluster_7, since Xp_GTX0501_2_Cluster_6 had two core genes
ra<-data.frame("TranscriptID"=rownames(filt_mat_core)) %>% left_join(antismash_core) %>%
filter(TranscriptID!="XANPAGTX0501_001694-T1"|Cluster!="Xp_GTX0501_2_Cluster_6") %>%
select(Description)
ra_colors = c("fungal-RiPP-like"= brewer.pal(8,"Dark2")[1], "NRP-metallophore"= brewer.pal(8,"Dark2")[4], "NRPS"= brewer.pal(8,"Dark2")[3],
"NRPS-like"= brewer.pal(8,"Dark2")[5], "NRPS,T1PKS"= brewer.pal(8,"Dark2")[7], "T1PKS"= brewer.pal(8,"Dark2")[6],
"T3PKS" = brewer.pal(8,"Dark2")[8], "terpene"= brewer.pal(8,"Dark2")[2])
ra = rowAnnotation(df = ra,col = list(Description = ra_colors))
HM_core = Heatmap(filt_mat_core, show_row_names = F, show_column_names = T,
row_title_rot = 0, col=col_fun, show_heatmap_legend = FALSE,
cluster_columns = FALSE,column_order = colord,
column_names_gp = gpar(fontsize = 6, font="Arial"),
row_title_gp = gpar(fontsize = 7, font="Arial"),
top_annotation = ta,
right_annotation = ra)
## Warning in validGP(list(...)): NAs introduced by coercion
## Warning in validGP(list(...)): NAs introduced by coercion
pdf(file="../results/all_core_SM_heatmap.pdf",width=8,height=8)
draw(HM_core)
dev.off()
## quartz_off_screen
## 2
#get order of the rows in the heatmap and match to b values
rord = row_order(HM_core)
## Warning: The heatmap has not been initialized. You might have different results
## if you repeatedly execute this function, e.g. when row_km/column_km was
## set. It is more suggested to do as `ht = draw(ht); row_order(ht)`.
rord<-rownames(filt_mat_core)[rord]
core_dge<-data.frame("TranscriptID"=rord) %>% left_join(antismash_core) %>%
filter(TranscriptID!="XANPAGTX0501_001694-T1"|Cluster!="Xp_GTX0501_2_Cluster_6") %>%
select(TranscriptID,b,Description)
head(core_dge)
## TranscriptID b Description
## 1 XANPAGTX0501_001972-T1 2.363522 NRPS
## 2 XANPAGTX0501_001973-T1 2.358272 T1PKS
## 3 XANPAGTX0501_009715-T1 2.760824 fungal-RiPP-like
## 4 XANPAGTX0501_009716-T1 2.958263 fungal-RiPP-like
## 5 XANPAGTX0501_009866-T1 NA terpene
## 6 XANPAGTX0501_001064-T1 -1.531609 fungal-RiPP-like
cl_int<-read.delim2("../../04_secretome/analysis_and_temp_files/05_cluster_structures/clustering_results.txt") %>% filter(ClusterID %in% c("cl04","cl16","cl18","cl19","cl20","cl21","cl22","cl23",
"cl24","cl24a","cl37","cl38","cl40","cl41","cl42","cl80",
"cl29","cl34"),Gene_Expression!="Non-DGE")
filt_mat_int<-subset(trans_mat, rownames(trans_mat) %in% cl_int$ProteinID)
#define row annotation
ra2<-data.frame("ProteinID"=rownames(filt_mat_int)) %>% left_join(cl_int) %>%
select(ClusterID)
#define color to match the tree
col_cl<-read.delim2("../../04_secretome/analysis_and_temp_files/05_cluster_structures/cluster_col.txt",sep=",") %>% filter(cluster_id %in% cl_int$ClusterID)
ra2_colors<-as.character(col_cl$color)
names(ra2_colors)<-as.character(col_cl$cluster_id)
ra2 = rowAnnotation(df = ra2,col = list(ClusterID = ra2_colors),show_legend = F)
ta2 = HeatmapAnnotation(df=s2c,col = list(condition = ta_colors),show_legend = F)
HM_int = Heatmap(filt_mat_int, show_row_names = T, show_column_names = T,
row_title_rot = 0, col=col_fun, show_heatmap_legend = F,
cluster_columns = FALSE,column_order = colord,
top_annotation = ta2,
right_annotation = ra2,
column_names_gp = gpar(fontsize = 6),
row_names_gp = gpar(fontsize = 6))
pdf(file="../results/all_secretome_int_heatmap.pdf",width=4,height=4)
draw(HM_int)
dev.off()
## quartz_off_screen
## 2
#get order of rows to match to clusters
rord = row_order(HM_int)
## Warning: The heatmap has not been initialized. You might have different results
## if you repeatedly execute this function, e.g. when row_km/column_km was
## set. It is more suggested to do as `ht = draw(ht); row_order(ht)`.
rord<-rownames(filt_mat_int)[rord]
rord2<-data.frame("ProteinID"=rord) %>% left_join(cl_int)
#get number of DGE per cluster of interest
t<-read.delim2("../../04_secretome/analysis_and_temp_files/05_cluster_structures/clustering_results.txt") %>% filter(ClusterID %in% c("cl04","cl16","cl18","cl19","cl20","cl21","cl22","cl23",
"cl24","cl24a","cl37","cl38","cl40","cl41","cl42","cl80",
"cl29","cl34"))
t%>% group_by(ClusterID,Gene_Expression) %>% summarise(n=n()) %>%
pivot_wider(names_from = Gene_Expression,values_from = n,values_fill=0)
## # A tibble: 18 × 3
## # Groups: ClusterID [18]
## ClusterID `Non-DGE` `Upregulated in lichen`
## <chr> <int> <int>
## 1 cl04 6 2
## 2 cl16 2 0
## 3 cl18 2 4
## 4 cl19 3 1
## 5 cl20 7 0
## 6 cl21 4 1
## 7 cl22 0 2
## 8 cl23 2 1
## 9 cl24 5 4
## 10 cl24a 6 5
## 11 cl29 3 1
## 12 cl34 3 1
## 13 cl37 1 1
## 14 cl38 3 1
## 15 cl40 1 1
## 16 cl41 0 3
## 17 cl42 0 1
## 18 cl80 1 1
../analysis_and_temp_files/09_dge_architecture/write.table(geneList5,'../analysis_and_temp_files/08_dge_culture_lichen/lichen_upregulated.txt',col.names = F,row.names = F,quote = F)
write.table(geneList6,'../analysis_and_temp_files/08_dge_culture_lichen/culture_upregulated.txt',col.names = F,row.names = F,quote = F)
perl croc.pl –reg ~/Documents/Lichen_project_TSL/03_transcriptomic_analysis/analysis_and_temp_files/08_dge_culture_lichen/culture_upregulated.txt –ref ~/Documents/Lichen_project_TSL/03_transcriptomic_analysis/analysis_and_temp_files/09_dge_architecture/reference.txt
* In lichen-upregulated genes, got 92 clusters. 12 of them have only 3 genes, and 83 <10 genes. Maximum count is 19
```r
croc_l<-read.delim("../analysis_and_temp_files/08_dge_culture_lichen/croc_lichen_upregulated.txt",header=F)
croc_l$cluster<-paste0("cluster",1:nrow(croc_l))
croc_l<-croc_l %>% separate_longer_delim(V9, delim = " ") %>% filter(V9!="") %>%
select(-c(V7,V8,V2,V3))
colnames(croc_l)<-c("contig","start","end","pval","TranscriptID","cluster")
croc_l %>% group_by(cluster) %>% summarize(n=n()) %>% arrange(desc(n)) %>% head()
## # A tibble: 6 × 2
## cluster n
## <chr> <int>
## 1 cluster11 19
## 2 cluster9 17
## 3 cluster52 16
## 4 cluster42 14
## 5 cluster92 14
## 6 cluster34 12
croc_l2<-croc_l %>% left_join(funannot2) %>%
select(cluster,TranscriptID, InterPro_new,secreted_consensus,antiSMASH)
## Joining with `by = join_by(TranscriptID)`
croc_l2 %>%
kable(format = "html", col.names = colnames(croc_l2)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "300px")
| cluster | TranscriptID | InterPro_new | secreted_consensus | antiSMASH |
|---|---|---|---|---|
| cluster1 | XANPAGTX0501_000227-T1 | IPR001251 CRAL-TRIO lipid binding domain, IPR011074 CRAL/TRIO, N-terminal domain, IPR036273 CRAL/TRIO, N-terminal domain superfamily, IPR036865 CRAL-TRIO lipid binding domain superfamily | FALSE | NA |
| cluster1 | XANPAGTX0501_000228-T1 | IPR008949 Isoprenoid synthase domain superfamily | FALSE | NA |
| cluster1 | XANPAGTX0501_000229-T1 | NA | FALSE | NA |
| cluster1 | XANPAGTX0501_000230-T1 | IPR000092 Polyprenyl synthetase, IPR008949 Isoprenoid synthase domain superfamily, IPR033749 Polyprenyl synthetase, conserved site | FALSE | NA |
| cluster2 | XANPAGTX0501_000414-T1 | NA | FALSE | NA |
| cluster2 | XANPAGTX0501_000413-T1 | NA | FALSE | NA |
| cluster2 | XANPAGTX0501_000420-T1 | IPR013087 Zinc finger C2H2-type | FALSE | NA |
| cluster2 | XANPAGTX0501_000417-T1 | NA | FALSE | NA |
| cluster3 | XANPAGTX0501_000443-T1 | IPR001680 WD40 repeat, IPR007111 NACHT nucleoside triphosphatase, IPR007751 Domain of unknown function DUF676, lipase-like, IPR011044 Quinoprotein amine dehydrogenase, beta chain-like, IPR011047 Quinoprotein alcohol dehydrogenase-like superfamily, IPR012908 GPI inositol-deacylase PGAP1-like, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR029058 Alpha/Beta hydrolase fold, IPR036322 WD40-repeat-containing domain superfamily | FALSE | NA |
| cluster3 | XANPAGTX0501_000443-T2 | IPR001680 WD40 repeat, IPR007111 NACHT nucleoside triphosphatase, IPR007751 Domain of unknown function DUF676, lipase-like, IPR011044 Quinoprotein amine dehydrogenase, beta chain-like, IPR011047 Quinoprotein alcohol dehydrogenase-like superfamily, IPR012908 GPI inositol-deacylase PGAP1-like, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR029058 Alpha/Beta hydrolase fold, IPR036322 WD40-repeat-containing domain superfamily | FALSE | NA |
| cluster3 | XANPAGTX0501_000447-T1 | NA | FALSE | NA |
| cluster3 | XANPAGTX0501_000448-T1 | NA | FALSE | NA |
| cluster4 | XANPAGTX0501_000576-T1 | IPR006162 Phosphopantetheine attachment site, IPR013968 Polyketide synthase, ketoreductase domain, IPR020806 Polyketide synthase, phosphopantetheine-binding domain, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily | FALSE | NA |
| cluster4 | XANPAGTX0501_000577-T1 | IPR011032 GroES-like superfamily, IPR013217 Methyltransferase type 12, IPR013968 Polyketide synthase, ketoreductase domain, IPR020807 Polyketide synthase, dehydratase domain, IPR020843 Polyketide synthase, enoylreductase domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036291 NAD(P)-binding domain superfamily, IPR042104 Polyketide synthase, dehydratase domain superfamily | FALSE | NA |
| cluster4 | XANPAGTX0501_000578-T1 | IPR001227 Acyl transferase domain superfamily, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016036 Malonyl-CoA ACP transacylase, ACP-binding, IPR016039 Thiolase-like, IPR020801 None, IPR020807 Polyketide synthase, dehydratase domain, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR032821 Polyketide synthase, C-terminal extension, IPR042104 Polyketide synthase, dehydratase domain superfamily | FALSE | NA |
| cluster4 | XANPAGTX0501_000579-T1 | IPR001227 Acyl transferase domain superfamily, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016039 Thiolase-like, IPR018201 Beta-ketoacyl synthase, active site, IPR020801 None, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR032821 Polyketide synthase, C-terminal extension | FALSE | NA |
| cluster5 | XANPAGTX0501_000601-T1 | NA | FALSE | NA |
| cluster5 | XANPAGTX0501_000606-T1 | NA | TRUE | NA |
| cluster5 | XANPAGTX0501_000602-T1 | NA | FALSE | NA |
| cluster5 | XANPAGTX0501_000610-T1 | NA | FALSE | NA |
| cluster5 | XANPAGTX0501_000604-T1 | NA | FALSE | NA |
| cluster5 | XANPAGTX0501_000605-T1 | NA | FALSE | NA |
| cluster5 | XANPAGTX0501_000609-T1 | NA | TRUE | NA |
| cluster5 | XANPAGTX0501_000603-T1 | IPR006076 FAD dependent oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | FALSE | NA |
| cluster6 | XANPAGTX0501_000650-T1 | NA | FALSE | NA |
| cluster6 | XANPAGTX0501_000655-T1 | IPR035992 Ricin B-like lectins | TRUE | NA |
| cluster6 | XANPAGTX0501_000649-T1 | NA | FALSE | NA |
| cluster6 | XANPAGTX0501_000656-T1 | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | TRUE | NA |
| cluster6 | XANPAGTX0501_000647-T1 | IPR000571 Zinc finger, CCCH-type | FALSE | NA |
| cluster6 | XANPAGTX0501_000648-T1 | IPR022099 Domain of unknown function DUF3638, IPR022105 Domain of unknown function DUF3645, IPR027417 P-loop containing nucleoside triphosphate hydrolase | FALSE | NA |
| cluster6 | XANPAGTX0501_000654-T1 | IPR004843 Calcineurin-like phosphoesterase domain, ApaH type, IPR029052 Metallo-dependent phosphatase-like | FALSE | NA |
| cluster7 | XANPAGTX0501_000758-T1 | IPR000757 Glycoside hydrolase family 16, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily | FALSE | NA |
| cluster7 | XANPAGTX0501_000751-T1 | NA | FALSE | NA |
| cluster7 | XANPAGTX0501_000757-T1 | IPR001173 Glycosyltransferase 2-like, IPR029044 Nucleotide-diphospho-sugar transferases | FALSE | NA |
| cluster7 | XANPAGTX0501_000755-T1 | NA | FALSE | NA |
| cluster8 | XANPAGTX0501_000872-T1 | NA | FALSE | NA |
| cluster8 | XANPAGTX0501_000873-T1 | IPR002347 Short-chain dehydrogenase/reductase SDR, IPR020904 Short-chain dehydrogenase/reductase, conserved site, IPR036291 NAD(P)-binding domain superfamily | FALSE | NA |
| cluster8 | XANPAGTX0501_000874-T1 | IPR001525 C-5 cytosine methyltransferase, IPR018117 DNA methylase, C-5 cytosine-specific, active site, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR031303 DNA methylase, C-5 cytosine-specific, conserved site | FALSE | NA |
| cluster8 | XANPAGTX0501_000879-T1 | IPR005198 Glycoside hydrolase, family 76, IPR008928 Six-hairpin glycosidase superfamily, IPR014480 Mannan endo-1,6-alpha-mannosidase | FALSE | NA |
| cluster9 | XANPAGTX0501_000922-T1 | NA | FALSE | Cluster_2 |
| cluster9 | XANPAGTX0501_000911-T1 | IPR002110 Ankyrin repeat, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster9 | XANPAGTX0501_000916-T1 | NA | FALSE | Cluster_2 |
| cluster9 | XANPAGTX0501_000914-T1 | NA | FALSE | Cluster_2 |
| cluster9 | XANPAGTX0501_000888-T1 | NA | FALSE | NA |
| cluster9 | XANPAGTX0501_000909-T1 | NA | FALSE | NA |
| cluster9 | XANPAGTX0501_000899-T1 | NA | FALSE | NA |
| cluster9 | XANPAGTX0501_000891-T1 | NA | FALSE | NA |
| cluster9 | XANPAGTX0501_000910-T1 | NA | FALSE | NA |
| cluster9 | XANPAGTX0501_000892-T1 | NA | FALSE | NA |
| cluster9 | XANPAGTX0501_000894-T1 | IPR027417 P-loop containing nucleoside triphosphate hydrolase | FALSE | NA |
| cluster9 | XANPAGTX0501_000917-T1 | NA | FALSE | Cluster_2 |
| cluster9 | XANPAGTX0501_000915-T1 | NA | FALSE | Cluster_2 |
| cluster9 | XANPAGTX0501_000897-T1 | IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily | FALSE | NA |
| cluster9 | XANPAGTX0501_000923-T1 | IPR008963 Purple acid phosphatase-like, N-terminal, IPR018946 PhoD-like phosphatase, metallophosphatase domain, IPR032093 Phospholipase D, N-terminal, IPR038607 PhoD-like superfamily | TRUE | Cluster_2 |
| cluster9 | XANPAGTX0501_000908-T1 | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR011008 Dimeric alpha-beta barrel, IPR025444 Monooxygenase af470-like, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily | FALSE | NA |
| cluster9 | XANPAGTX0501_000913-T1 | NA | FALSE | Cluster_2 |
| cluster10 | XANPAGTX0501_000949-T1 | NA | FALSE | NA |
| cluster10 | XANPAGTX0501_000948-T1 | NA | FALSE | NA |
| cluster10 | XANPAGTX0501_000952-T1 | NA | FALSE | NA |
| cluster10 | XANPAGTX0501_000951-T1 | NA | FALSE | NA |
| cluster11 | XANPAGTX0501_006311-T1 | NA | FALSE | Cluster_2 |
| cluster11 | XANPAGTX0501_006293-T1 | IPR001958 Tetracycline resistance protein TetA/multidrug resistance protein MdtG, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006324-T1 | IPR001204 Phosphate transporter | FALSE | Cluster_2 |
| cluster11 | XANPAGTX0501_006295-T1 | IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006314-T1 | IPR001646 Pentapeptide repeat | FALSE | Cluster_2 |
| cluster11 | XANPAGTX0501_006301-T1 | IPR001585 Transaldolase/Fructose-6-phosphate aldolase, IPR013785 Aldolase-type TIM barrel, IPR018225 Transaldolase, active site | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006302-T1 | IPR036291 NAD(P)-binding domain superfamily | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006298-T1 | IPR005123 Oxoglutarate/iron-dependent dioxygenase, IPR026992 Non-haem dioxygenase N-terminal domain, IPR027443 Isopenicillin N synthase-like superfamily | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006320-T1 | NA | FALSE | Cluster_2 |
| cluster11 | XANPAGTX0501_006319-T1 | IPR001031 Thioesterase, IPR001227 Acyl transferase domain superfamily, IPR006162 Phosphopantetheine attachment site, IPR009081 Phosphopantetheine binding ACP domain, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016036 Malonyl-CoA ACP transacylase, ACP-binding, IPR016039 Thiolase-like, IPR018201 Beta-ketoacyl synthase, active site, IPR020801 None, IPR020806 Polyketide synthase, phosphopantetheine-binding domain, IPR020807 Polyketide synthase, dehydratase domain, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR029058 Alpha/Beta hydrolase fold, IPR030918 Polyketide product template domain, IPR032088 Starter unit:ACP transacylase, IPR036736 ACP-like superfamily, IPR042104 Polyketide synthase, dehydratase domain superfamily | FALSE | Cluster_2 |
| cluster11 | XANPAGTX0501_006304-T1 | NA | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006317-T1 | IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | Cluster_2 |
| cluster11 | XANPAGTX0501_006318-T1 | IPR009799 EthD domain, IPR011008 Dimeric alpha-beta barrel | FALSE | Cluster_2 |
| cluster11 | XANPAGTX0501_006303-T1 | NA | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006294-T1 | NA | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006308-T1 | NA | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006296-T1 | IPR001173 Glycosyltransferase 2-like, IPR029044 Nucleotide-diphospho-sugar transferases | FALSE | Cluster_1 |
| cluster11 | XANPAGTX0501_006291-T1 | NA | TRUE | Cluster_1 |
| cluster11 | XANPAGTX0501_006292-T1 | NA | TRUE | Cluster_1 |
| cluster12 | XANPAGTX0501_006907-T1 | IPR041622 SMODS and SLOG-associating 2TM effector domain, fungi | FALSE | NA |
| cluster12 | XANPAGTX0501_006918-T1 | IPR010255 Haem peroxidase superfamily, IPR017972 Cytochrome P450, conserved site, IPR019791 Haem peroxidase, animal-type, IPR034812 Psi-factor producing oxygenase, N-terminal heme peroxidase domain, IPR036396 Cytochrome P450 superfamily | FALSE | NA |
| cluster12 | XANPAGTX0501_006903-T1 | NA | FALSE | NA |
| cluster12 | XANPAGTX0501_006917-T1 | IPR018712 Domain of unknown function DUF2235 | FALSE | NA |
| cluster12 | XANPAGTX0501_006919-T1 | NA | FALSE | NA |
| cluster12 | XANPAGTX0501_006904-T1 | NA | FALSE | NA |
| cluster12 | XANPAGTX0501_006910-T1 | NA | FALSE | NA |
| cluster12 | XANPAGTX0501_006906-T1 | IPR024498 Domain of unknown function DUF2786 | FALSE | NA |
| cluster12 | XANPAGTX0501_006909-T1 | NA | FALSE | NA |
| cluster12 | XANPAGTX0501_006921-T1 | NA | FALSE | NA |
| cluster12 | XANPAGTX0501_006922-T1 | IPR004313 Acireductone dioxygenase ARD family, IPR011051 RmlC-like cupin domain superfamily, IPR014710 RmlC-like jelly roll fold, IPR027496 Acireductone dioxygenase, eukaryotes | FALSE | NA |
| cluster13 | XANPAGTX0501_006951-T1 | NA | FALSE | NA |
| cluster13 | XANPAGTX0501_006950-T1 | NA | FALSE | NA |
| cluster13 | XANPAGTX0501_006945-T1 | NA | FALSE | NA |
| cluster13 | XANPAGTX0501_006946-T1 | NA | FALSE | NA |
| cluster13 | XANPAGTX0501_006957-T1 | NA | FALSE | NA |
| cluster13 | XANPAGTX0501_006953-T1 | NA | FALSE | NA |
| cluster14 | XANPAGTX0501_006970-T1 | NA | FALSE | NA |
| cluster14 | XANPAGTX0501_006972-T1 | NA | FALSE | NA |
| cluster14 | XANPAGTX0501_006967-T1 | NA | TRUE | NA |
| cluster14 | XANPAGTX0501_006971-T1 | NA | FALSE | NA |
| cluster14 | XANPAGTX0501_006974-T1 | NA | FALSE | NA |
| cluster15 | XANPAGTX0501_007248-T1 | IPR019313 Mediator complex, subunit Med17 | FALSE | NA |
| cluster15 | XANPAGTX0501_007251-T1 | IPR007111 NACHT nucleoside triphosphatase, IPR027417 P-loop containing nucleoside triphosphate hydrolase | FALSE | NA |
| cluster15 | XANPAGTX0501_007247-T1 | IPR000023 Phosphofructokinase domain, IPR012003 ATP-dependent 6-phosphofructokinase, prokaryotic-type, IPR015912 Phosphofructokinase, conserved site, IPR022953 ATP-dependent 6-phosphofructokinase, IPR035966 Phosphofructokinase superfamily | FALSE | NA |
| cluster15 | XANPAGTX0501_007245-T1 | NA | FALSE | NA |
| cluster15 | XANPAGTX0501_007244-T1 | NA | FALSE | NA |
| cluster15 | XANPAGTX0501_007246-T1 | IPR000023 Phosphofructokinase domain, IPR015912 Phosphofructokinase, conserved site, IPR022953 ATP-dependent 6-phosphofructokinase, IPR035966 Phosphofructokinase superfamily | FALSE | NA |
| cluster15 | XANPAGTX0501_007242-T1 | NA | FALSE | NA |
| cluster15 | XANPAGTX0501_007253-T1 | NA | FALSE | NA |
| cluster16 | XANPAGTX0501_007271-T1 | IPR002347 Short-chain dehydrogenase/reductase SDR, IPR036291 NAD(P)-binding domain superfamily | FALSE | Cluster_1 |
| cluster16 | XANPAGTX0501_007267-T1 | IPR001077 O-methyltransferase domain, IPR016461 O-methyltransferase COMT-type, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | Cluster_1 |
| cluster16 | XANPAGTX0501_007272-T1 | NA | TRUE | Cluster_1 |
| cluster16 | XANPAGTX0501_007268-T1 | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR016167 FAD-binding, type PCMH, subdomain 1, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | TRUE | Cluster_1 |
| cluster17 | XANPAGTX0501_007313-T1 | NA | FALSE | NA |
| cluster17 | XANPAGTX0501_007308-T1 | NA | FALSE | NA |
| cluster17 | XANPAGTX0501_007303-T1 | IPR018712 Domain of unknown function DUF2235, IPR029058 Alpha/Beta hydrolase fold, IPR036404 Jacalin-like lectin domain superfamily | FALSE | NA |
| cluster17 | XANPAGTX0501_007310-T1 | IPR002151 Kinesin light chain, IPR011990 Tetratricopeptide-like helical domain superfamily, IPR013026 None, IPR013087 Zinc finger C2H2-type, IPR019734 Tetratricopeptide repeat | FALSE | NA |
| cluster17 | XANPAGTX0501_007312-T1 | NA | FALSE | NA |
| cluster17 | XANPAGTX0501_007311-T1 | IPR002182 NB-ARC, IPR010730 Heterokaryon incompatibility, IPR011990 Tetratricopeptide-like helical domain superfamily, IPR013026 None, IPR019734 Tetratricopeptide repeat, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR031352 NACHT-NTPase and P-loop NTPases, N-terminal domain, IPR041664 Orc1-like, AAA ATPase domain | FALSE | NA |
| cluster17 | XANPAGTX0501_007309-T1 | IPR040976 Fungal-type protein kinase | FALSE | NA |
| cluster18 | XANPAGTX0501_007344-T1 | NA | FALSE | Cluster_2 |
| cluster18 | XANPAGTX0501_007361-T1 | NA | FALSE | Cluster_2 |
| cluster18 | XANPAGTX0501_007362-T1 | NA | TRUE | Cluster_2 |
| cluster18 | XANPAGTX0501_007353-T1 | NA | FALSE | Cluster_2 |
| cluster18 | XANPAGTX0501_007349-T1 | NA | FALSE | Cluster_2 |
| cluster18 | XANPAGTX0501_007351-T1 | IPR000873 AMP-dependent synthetase/ligase domain, IPR001242 Condensation domain, IPR009081 Phosphopantetheine binding ACP domain, IPR020845 AMP-binding, conserved site, IPR023213 Chloramphenicol acetyltransferase-like domain superfamily, IPR025110 AMP-binding enzyme, C-terminal domain, IPR036736 ACP-like superfamily, IPR042099 ANL, N-terminal domain | FALSE | Cluster_2 |
| cluster18 | XANPAGTX0501_007352-T1 | IPR000873 AMP-dependent synthetase/ligase domain, IPR001242 Condensation domain, IPR009081 Phosphopantetheine binding ACP domain, IPR020845 AMP-binding, conserved site, IPR023213 Chloramphenicol acetyltransferase-like domain superfamily, IPR025110 AMP-binding enzyme, C-terminal domain, IPR036736 ACP-like superfamily, IPR042099 ANL, N-terminal domain | FALSE | Cluster_2 |
| cluster18 | XANPAGTX0501_007350-T1 | IPR020845 AMP-binding, conserved site, IPR042099 ANL, N-terminal domain | FALSE | Cluster_2 |
| cluster18 | XANPAGTX0501_007343-T1 | NA | FALSE | Cluster_2 |
| cluster19 | XANPAGTX0501_007397-T1 | NA | FALSE | Cluster_3 |
| cluster19 | XANPAGTX0501_007403-T1 | NA | FALSE | NA |
| cluster19 | XANPAGTX0501_007404-T1 | IPR001002 Chitin-binding, type 1, IPR001223 Glycoside hydrolase family 18, catalytic domain, IPR011583 Chitinase II, IPR017853 Glycoside hydrolase superfamily, IPR036861 Endochitinase-like superfamily | FALSE | NA |
| cluster19 | XANPAGTX0501_007405-T1 | IPR001002 Chitin-binding, type 1, IPR002509 NodB homology domain, IPR011330 Glycoside hydrolase/deacetylase, beta/alpha-barrel, IPR017853 Glycoside hydrolase superfamily, IPR018371 Chitin-binding, type 1, conserved site, IPR029070 Chitinase insertion domain superfamily, IPR036852 Peptidase S8/S53 domain superfamily, IPR036861 Endochitinase-like superfamily | FALSE | NA |
| cluster20 | XANPAGTX0501_007872-T1 | NA | FALSE | Cluster_1 |
| cluster20 | XANPAGTX0501_007870-T1 | NA | FALSE | Cluster_1 |
| cluster20 | XANPAGTX0501_007865-T1 | NA | TRUE | NA |
| cluster20 | XANPAGTX0501_007863-T1 | NA | FALSE | NA |
| cluster20 | XANPAGTX0501_007866-T1 | NA | FALSE | NA |
| cluster20 | XANPAGTX0501_007862-T1 | NA | FALSE | NA |
| cluster20 | XANPAGTX0501_007864-T1 | NA | FALSE | NA |
| cluster20 | XANPAGTX0501_007873-T1 | NA | FALSE | Cluster_1 |
| cluster20 | XANPAGTX0501_007869-T1 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | FALSE | Cluster_1 |
| cluster21 | XANPAGTX0501_007923-T1 | IPR000608 Ubiquitin-conjugating enzyme E2, IPR016135 Ubiquitin-conjugating enzyme/RWD-like | FALSE | NA |
| cluster21 | XANPAGTX0501_007933-T1 | NA | FALSE | NA |
| cluster21 | XANPAGTX0501_007932-T1 | NA | FALSE | NA |
| cluster21 | XANPAGTX0501_007929-T1 | NA | FALSE | NA |
| cluster21 | XANPAGTX0501_007931-T1 | NA | FALSE | NA |
| cluster21 | XANPAGTX0501_007934-T1 | NA | FALSE | NA |
| cluster21 | XANPAGTX0501_007930-T1 | NA | FALSE | NA |
| cluster21 | XANPAGTX0501_007939-T1 | NA | TRUE | NA |
| cluster22 | XANPAGTX0501_007969-T1 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE | NA |
| cluster22 | XANPAGTX0501_007973-T1 | NA | FALSE | NA |
| cluster22 | XANPAGTX0501_007970-T1 | IPR001077 O-methyltransferase domain, IPR016461 O-methyltransferase COMT-type, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | NA |
| cluster22 | XANPAGTX0501_007972-T1 | NA | FALSE | NA |
| cluster22 | XANPAGTX0501_007971-T1 | NA | FALSE | NA |
| cluster22 | XANPAGTX0501_007976-T1 | NA | TRUE | NA |
| cluster23 | XANPAGTX0501_008007-T1 | NA | FALSE | NA |
| cluster23 | XANPAGTX0501_008008-T1 | NA | FALSE | NA |
| cluster23 | XANPAGTX0501_008009-T1 | NA | FALSE | NA |
| cluster24 | XANPAGTX0501_008019-T1 | NA | TRUE | NA |
| cluster24 | XANPAGTX0501_008029-T1 | NA | FALSE | NA |
| cluster24 | XANPAGTX0501_008031-T1 | NA | FALSE | NA |
| cluster24 | XANPAGTX0501_008032-T1 | NA | FALSE | NA |
| cluster24 | XANPAGTX0501_008024-T2 | IPR007192 Cdc23, IPR011990 Tetratricopeptide-like helical domain superfamily, IPR013026 None, IPR019734 Tetratricopeptide repeat | FALSE | NA |
| cluster24 | XANPAGTX0501_008030-T1 | IPR001128 Cytochrome P450, IPR002401 Cytochrome P450, E-class, group I, IPR017972 Cytochrome P450, conserved site, IPR036396 Cytochrome P450 superfamily | FALSE | NA |
| cluster24 | XANPAGTX0501_008041-T1 | NA | TRUE | NA |
| cluster24 | XANPAGTX0501_008027-T1 | IPR000028 Chloroperoxidase, IPR036851 Chloroperoxidase-like superfamily | TRUE | NA |
| cluster24 | XANPAGTX0501_008018-T1 | NA | FALSE | NA |
| cluster24 | XANPAGTX0501_008028-T1 | NA | FALSE | NA |
| cluster25 | XANPAGTX0501_008272-T1 | IPR000873 AMP-dependent synthetase/ligase domain, IPR006162 Phosphopantetheine attachment site, IPR009081 Phosphopantetheine binding ACP domain, IPR013120 Fatty acyl-coenzyme A reductase, NAD-binding domain, IPR020845 AMP-binding, conserved site, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR042099 ANL, N-terminal domain | FALSE | Cluster_1 |
| cluster25 | XANPAGTX0501_008267-T1 | IPR024079 Metallopeptidase, catalytic domain superfamily | FALSE | Cluster_1 |
| cluster25 | XANPAGTX0501_008268-T1 | NA | FALSE | Cluster_1 |
| cluster25 | XANPAGTX0501_008274-T1 | NA | FALSE | Cluster_1 |
| cluster25 | XANPAGTX0501_008270-T1 | NA | TRUE | Cluster_1 |
| cluster25 | XANPAGTX0501_008273-T1 | IPR000873 AMP-dependent synthetase/ligase domain, IPR006162 Phosphopantetheine attachment site, IPR009081 Phosphopantetheine binding ACP domain, IPR013120 Fatty acyl-coenzyme A reductase, NAD-binding domain, IPR020845 AMP-binding, conserved site, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR042099 ANL, N-terminal domain | FALSE | Cluster_1 |
| cluster26 | XANPAGTX0501_008284-T1 | IPR029044 Nucleotide-diphospho-sugar transferases | FALSE | Cluster_1 |
| cluster26 | XANPAGTX0501_008288-T1 | NA | FALSE | NA |
| cluster26 | XANPAGTX0501_008289-T1 | NA | FALSE | NA |
| cluster26 | XANPAGTX0501_008291-T1 | NA | FALSE | NA |
| cluster27 | XANPAGTX0501_008409-T1 | IPR001680 WD40 repeat, IPR011659 WD40-like beta propeller, IPR011990 Tetratricopeptide-like helical domain superfamily, IPR013026 None, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR017986 None, IPR019734 Tetratricopeptide repeat, IPR019775 WD40 repeat, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR036322 WD40-repeat-containing domain superfamily | FALSE | NA |
| cluster27 | XANPAGTX0501_008413-T1 | NA | FALSE | NA |
| cluster27 | XANPAGTX0501_008414-T1 | NA | FALSE | NA |
| cluster27 | XANPAGTX0501_008417-T1 | IPR002347 Short-chain dehydrogenase/reductase SDR, IPR020904 Short-chain dehydrogenase/reductase, conserved site, IPR036291 NAD(P)-binding domain superfamily | FALSE | NA |
| cluster27 | XANPAGTX0501_008418-T1 | IPR023213 Chloramphenicol acetyltransferase-like domain superfamily | FALSE | NA |
| cluster28 | XANPAGTX0501_008435-T1 | IPR000073 Alpha/beta hydrolase fold-1, IPR013595 Peptidase S33 tripeptidyl aminopeptidase-like, C-terminal, IPR029058 Alpha/Beta hydrolase fold | FALSE | NA |
| cluster28 | XANPAGTX0501_008438-T1 | NA | FALSE | NA |
| cluster28 | XANPAGTX0501_008437-T1 | IPR042099 ANL, N-terminal domain | FALSE | NA |
| cluster28 | XANPAGTX0501_008439-T1 | IPR003819 TauD/TfdA-like domain, IPR042098 Taurine dioxygenase TauD-like superfamily | FALSE | NA |
| cluster28 | XANPAGTX0501_008436-T1 | NA | FALSE | NA |
| cluster29 | XANPAGTX0501_008541-T1 | NA | FALSE | NA |
| cluster29 | XANPAGTX0501_008525-T1 | NA | FALSE | NA |
| cluster29 | XANPAGTX0501_008533-T1 | NA | FALSE | NA |
| cluster29 | XANPAGTX0501_008529-T1 | NA | FALSE | NA |
| cluster29 | XANPAGTX0501_008534-T1 | NA | FALSE | NA |
| cluster30 | XANPAGTX0501_008676-T1 | NA | FALSE | NA |
| cluster30 | XANPAGTX0501_008677-T1 | IPR027417 P-loop containing nucleoside triphosphate hydrolase | FALSE | NA |
| cluster30 | XANPAGTX0501_008683-T1 | NA | TRUE | NA |
| cluster31 | XANPAGTX0501_008863-T1 | NA | FALSE | Cluster_1 |
| cluster31 | XANPAGTX0501_008852-T1 | IPR001227 Acyl transferase domain superfamily, IPR009081 Phosphopantetheine binding ACP domain, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016036 Malonyl-CoA ACP transacylase, ACP-binding, IPR016039 Thiolase-like, IPR020801 None, IPR020806 Polyketide synthase, phosphopantetheine-binding domain, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR030918 Polyketide product template domain, IPR032088 Starter unit:ACP transacylase, IPR032821 Polyketide synthase, C-terminal extension, IPR036736 ACP-like superfamily, IPR042104 Polyketide synthase, dehydratase domain superfamily | FALSE | Cluster_1 |
| cluster31 | XANPAGTX0501_008851-T1 | IPR001279 Metallo-beta-lactamase, IPR036866 Ribonuclease Z/Hydroxyacylglutathione hydrolase-like | FALSE | Cluster_1 |
| cluster31 | XANPAGTX0501_008856-T1 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily | FALSE | Cluster_1 |
| cluster31 | XANPAGTX0501_008850-T1 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR010929 CDR ABC transporter, IPR013525 ABC-2 type transporter, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR029481 ABC-transporter, N-terminal domain, IPR034001 ATP-binding cassette transporter, PDR-like subfamily G, domain 1, IPR034003 ATP-binding cassette transporter, PDR-like subfamily G, domain 2 | FALSE | Cluster_1 |
| cluster31 | XANPAGTX0501_008853-T1 | IPR009799 EthD domain, IPR011008 Dimeric alpha-beta barrel | FALSE | Cluster_1 |
| cluster31 | XANPAGTX0501_008855-T1 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | FALSE | Cluster_1 |
| cluster32 | XANPAGTX0501_008875-T1 | NA | TRUE | NA |
| cluster32 | XANPAGTX0501_008876-T1 | NA | FALSE | NA |
| cluster32 | XANPAGTX0501_008877-T1 | NA | FALSE | NA |
| cluster33 | XANPAGTX0501_009046-T1 | NA | FALSE | NA |
| cluster33 | XANPAGTX0501_009041-T1 | IPR002347 Short-chain dehydrogenase/reductase SDR, IPR036291 NAD(P)-binding domain superfamily | FALSE | NA |
| cluster33 | XANPAGTX0501_009040-T1 | NA | FALSE | NA |
| cluster33 | XANPAGTX0501_009055-T1 | IPR010730 Heterokaryon incompatibility | FALSE | NA |
| cluster33 | XANPAGTX0501_009052-T1 | NA | FALSE | NA |
| cluster33 | XANPAGTX0501_009054-T1 | NA | FALSE | NA |
| cluster33 | XANPAGTX0501_009050-T1 | NA | FALSE | NA |
| cluster34 | XANPAGTX0501_009194-T1 | IPR001077 O-methyltransferase domain, IPR016461 O-methyltransferase COMT-type, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | NA |
| cluster34 | XANPAGTX0501_009204-T1 | IPR001077 O-methyltransferase domain, IPR016461 O-methyltransferase COMT-type, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | NA |
| cluster34 | XANPAGTX0501_009201-T1 | NA | FALSE | NA |
| cluster34 | XANPAGTX0501_009192-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE | NA |
| cluster34 | XANPAGTX0501_009196-T1 | NA | FALSE | NA |
| cluster34 | XANPAGTX0501_009202-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE | NA |
| cluster34 | XANPAGTX0501_009199-T1 | NA | FALSE | NA |
| cluster34 | XANPAGTX0501_009189-T1 | NA | TRUE | NA |
| cluster34 | XANPAGTX0501_009193-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE | NA |
| cluster34 | XANPAGTX0501_009203-T1 | IPR001077 O-methyltransferase domain, IPR016461 O-methyltransferase COMT-type, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | NA |
| cluster34 | XANPAGTX0501_009205-T1 | NA | FALSE | NA |
| cluster34 | XANPAGTX0501_009195-T1 | NA | FALSE | NA |
| cluster35 | XANPAGTX0501_000971-T1 | IPR011009 Protein kinase-like domain superfamily | FALSE | NA |
| cluster35 | XANPAGTX0501_000972-T1 | NA | FALSE | NA |
| cluster35 | XANPAGTX0501_000974-T1 | IPR000573 Aconitase A/isopropylmalate dehydratase small subunit, swivel domain, IPR001030 Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain, IPR004418 Homoaconitase, mitochondrial, IPR015928 Aconitase/3-isopropylmalate dehydratase, swivel, IPR015931 Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3, IPR018136 Aconitase family, 4Fe-4S cluster binding site, IPR036008 Aconitase, iron-sulfur domain, IPR039386 Homoaconitase, swivel domain | FALSE | NA |
| cluster35 | XANPAGTX0501_000978-T1 | NA | FALSE | NA |
| cluster35 | XANPAGTX0501_000973-T1 | IPR000192 Aminotransferase class V domain, IPR015421 Pyridoxal phosphate-dependent transferase, major domain, IPR015422 Pyridoxal phosphate-dependent transferase, small domain, IPR015424 Pyridoxal phosphate-dependent transferase, IPR022278 Phosphoserine aminotransferase | FALSE | NA |
| cluster36 | XANPAGTX0501_001015-T1 | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | TRUE | NA |
| cluster36 | XANPAGTX0501_001008-T1 | NA | FALSE | NA |
| cluster36 | XANPAGTX0501_001017-T1 | IPR007111 NACHT nucleoside triphosphatase, IPR024983 CHAT domain, IPR027417 P-loop containing nucleoside triphosphate hydrolase | FALSE | NA |
| cluster36 | XANPAGTX0501_001010-T1 | NA | FALSE | NA |
| cluster36 | XANPAGTX0501_001014-T1 | NA | FALSE | NA |
| cluster37 | XANPAGTX0501_001063-T1 | NA | TRUE | Cluster_1 |
| cluster37 | XANPAGTX0501_001064-T1 | IPR021765 Mycotoxin biosynthesis protein UstYa-like | FALSE | Cluster_1 |
| cluster37 | XANPAGTX0501_001062-T1 | NA | FALSE | Cluster_1 |
| cluster37 | XANPAGTX0501_001061-T1 | IPR002328 Alcohol dehydrogenase, zinc-type, conserved site, IPR011032 GroES-like superfamily, IPR013149 Alcohol dehydrogenase-like, C-terminal, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR020843 Polyketide synthase, enoylreductase domain, IPR036291 NAD(P)-binding domain superfamily | FALSE | Cluster_1 |
| cluster38 | XANPAGTX0501_001178-T1 | NA | FALSE | NA |
| cluster38 | XANPAGTX0501_001183-T1 | NA | TRUE | NA |
| cluster38 | XANPAGTX0501_001184-T1 | NA | FALSE | NA |
| cluster38 | XANPAGTX0501_001185-T1 | NA | FALSE | NA |
| cluster39 | XANPAGTX0501_001458-T1 | IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 | TRUE | NA |
| cluster39 | XANPAGTX0501_001455-T1 | IPR005556 SUN family | TRUE | NA |
| cluster39 | XANPAGTX0501_001453-T1 | IPR010255 Haem peroxidase superfamily, IPR019791 Haem peroxidase, animal-type, IPR034812 Psi-factor producing oxygenase, N-terminal heme peroxidase domain, IPR036396 Cytochrome P450 superfamily, IPR037120 Haem peroxidase domain superfamily, animal type | FALSE | NA |
| cluster39 | XANPAGTX0501_001462-T1 | IPR008775 Phytanoyl-CoA dioxygenase-like | FALSE | NA |
| cluster39 | XANPAGTX0501_001452-T1 | IPR018712 Domain of unknown function DUF2235 | FALSE | NA |
| cluster39 | XANPAGTX0501_001451-T1 | NA | FALSE | NA |
| cluster39 | XANPAGTX0501_001465-T1 | NA | FALSE | NA |
| cluster39 | XANPAGTX0501_001448-T1 | IPR011701 Major facilitator superfamily, IPR036259 MFS transporter superfamily | FALSE | NA |
| cluster40 | XANPAGTX0501_001497-T1 | NA | FALSE | NA |
| cluster40 | XANPAGTX0501_001498-T1 | IPR012340 Nucleic acid-binding, OB-fold | FALSE | NA |
| cluster40 | XANPAGTX0501_001496-T1 | NA | FALSE | NA |
| cluster41 | XANPAGTX0501_001710-T1 | IPR007577 Glycosyltransferase, DXD sugar-binding motif, IPR029044 Nucleotide-diphospho-sugar transferases | FALSE | NA |
| cluster41 | XANPAGTX0501_001712-T1 | IPR001227 Acyl transferase domain superfamily, IPR006162 Phosphopantetheine attachment site, IPR009081 Phosphopantetheine binding ACP domain, IPR011032 GroES-like superfamily, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR013216 Methyltransferase type 11, IPR013217 Methyltransferase type 12, IPR013968 Polyketide synthase, ketoreductase domain, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016036 Malonyl-CoA ACP transacylase, ACP-binding, IPR016039 Thiolase-like, IPR018201 Beta-ketoacyl synthase, active site, IPR020801 None, IPR020806 Polyketide synthase, phosphopantetheine-binding domain, IPR020807 Polyketide synthase, dehydratase domain, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR020843 Polyketide synthase, enoylreductase domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR032821 Polyketide synthase, C-terminal extension, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR042104 Polyketide synthase, dehydratase domain superfamily | FALSE | NA |
| cluster41 | XANPAGTX0501_010750-T1 | NA | FALSE | NA |
| cluster41 | XANPAGTX0501_001713-T1 | IPR000073 Alpha/beta hydrolase fold-1, IPR005152 Lipase, secreted, IPR022742 Serine aminopeptidase, S33, IPR029058 Alpha/Beta hydrolase fold | FALSE | NA |
| cluster41 | XANPAGTX0501_001708-T1 | NA | TRUE | NA |
| cluster42 | XANPAGTX0501_009317-T1 | IPR008979 Galactose-binding-like domain superfamily | TRUE | NA |
| cluster42 | XANPAGTX0501_009340-T1 | NA | TRUE | NA |
| cluster42 | XANPAGTX0501_009318-T1 | IPR011333 SKP1/BTB/POZ domain superfamily | FALSE | NA |
| cluster42 | XANPAGTX0501_009342-T1 | NA | FALSE | NA |
| cluster42 | XANPAGTX0501_009341-T1 | NA | FALSE | NA |
| cluster42 | XANPAGTX0501_009322-T1 | NA | FALSE | NA |
| cluster42 | XANPAGTX0501_009326-T1 | NA | FALSE | NA |
| cluster42 | XANPAGTX0501_009321-T1 | NA | FALSE | NA |
| cluster42 | XANPAGTX0501_009316-T1 | IPR001810 F-box domain, IPR036047 F-box-like domain superfamily | FALSE | NA |
| cluster42 | XANPAGTX0501_009311-T1 | IPR008427 Extracellular membrane protein, CFEM domain | TRUE | NA |
| cluster42 | XANPAGTX0501_009320-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE | NA |
| cluster42 | XANPAGTX0501_009310-T1 | IPR032805 Wax synthase domain | FALSE | NA |
| cluster42 | XANPAGTX0501_009331-T1 | NA | FALSE | NA |
| cluster42 | XANPAGTX0501_009332-T1 | NA | FALSE | NA |
| cluster43 | XANPAGTX0501_009435-T1 | NA | FALSE | NA |
| cluster43 | XANPAGTX0501_009437-T1 | NA | FALSE | NA |
| cluster43 | XANPAGTX0501_009438-T1 | NA | FALSE | NA |
| cluster43 | XANPAGTX0501_009439-T1 | NA | FALSE | NA |
| cluster43 | XANPAGTX0501_009436-T1 | IPR000330 SNF2, N-terminal, IPR001650 Helicase, C-terminal, IPR001841 Zinc finger, RING-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR014001 Helicase superfamily 1/2, ATP-binding domain, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR038718 SNF2-like, N-terminal domain superfamily | FALSE | NA |
| cluster44 | XANPAGTX0501_009558-T1 | IPR000719 Protein kinase domain, IPR011009 Protein kinase-like domain superfamily, IPR036465 von Willebrand factor A-like domain superfamily | FALSE | NA |
| cluster44 | XANPAGTX0501_009557-T1 | IPR003615 HNH nuclease | FALSE | NA |
| cluster44 | XANPAGTX0501_009566-T1 | NA | FALSE | NA |
| cluster44 | XANPAGTX0501_009555-T1 | NA | FALSE | NA |
| cluster44 | XANPAGTX0501_009559-T1 | NA | FALSE | NA |
| cluster45 | XANPAGTX0501_009670-T1 | IPR000845 Nucleoside phosphorylase domain, IPR002110 Ankyrin repeat, IPR007111 NACHT nucleoside triphosphatase, IPR020683 Domain of unknown function DUF3447, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR035994 Nucleoside phosphorylase superfamily, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster45 | XANPAGTX0501_009672-T1 | NA | FALSE | NA |
| cluster45 | XANPAGTX0501_009671-T1 | NA | FALSE | NA |
| cluster45 | XANPAGTX0501_009668-T1 | NA | TRUE | NA |
| cluster45 | XANPAGTX0501_009673-T1 | IPR003593 AAA+ ATPase domain, IPR003959 ATPase, AAA-type, core, IPR027417 P-loop containing nucleoside triphosphate hydrolase | FALSE | NA |
| cluster45 | XANPAGTX0501_009669-T1 | IPR003689 Zinc/iron permease | FALSE | NA |
| cluster45 | XANPAGTX0501_009666-T1 | NA | FALSE | NA |
| cluster46 | XANPAGTX0501_009688-T1 | IPR000254 Cellulose-binding domain, fungal, IPR035971 Cellulose-binding domain superfamily, IPR036908 RlpA-like domain superfamily | TRUE | NA |
| cluster46 | XANPAGTX0501_009689-T1 | NA | TRUE | NA |
| cluster46 | XANPAGTX0501_009690-T1 | NA | TRUE | NA |
| cluster47 | XANPAGTX0501_009730-T1 | NA | TRUE | Cluster_1 |
| cluster47 | XANPAGTX0501_009731-T1 | IPR005197 Glycoside hydrolase family 71 | TRUE | Cluster_1 |
| cluster47 | XANPAGTX0501_009734-T1 | NA | FALSE | Cluster_1 |
| cluster47 | XANPAGTX0501_009738-T1 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | FALSE | NA |
| cluster48 | XANPAGTX0501_009872-T1 | NA | FALSE | Cluster_1 |
| cluster48 | XANPAGTX0501_009876-T1 | IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily | FALSE | NA |
| cluster48 | XANPAGTX0501_009883-T1 | NA | FALSE | NA |
| cluster48 | XANPAGTX0501_009887-T1 | NA | TRUE | NA |
| cluster48 | XANPAGTX0501_009875-T1 | NA | FALSE | NA |
| cluster48 | XANPAGTX0501_009886-T1 | NA | TRUE | NA |
| cluster48 | XANPAGTX0501_009881-T2 | IPR004212 GTF2I-like repeat | FALSE | NA |
| cluster48 | XANPAGTX0501_009873-T1 | NA | FALSE | Cluster_1 |
| cluster49 | XANPAGTX0501_010016-T2 | IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | FALSE | NA |
| cluster49 | XANPAGTX0501_010022-T1 | NA | TRUE | NA |
| cluster49 | XANPAGTX0501_010026-T1 | IPR018392 LysM domain, IPR036779 LysM domain superfamily | TRUE | NA |
| cluster49 | XANPAGTX0501_010021-T1 | NA | TRUE | NA |
| cluster49 | XANPAGTX0501_010016-T1 | IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | FALSE | NA |
| cluster49 | XANPAGTX0501_010023-T1 | NA | FALSE | NA |
| cluster49 | XANPAGTX0501_010027-T1 | NA | TRUE | NA |
| cluster50 | XANPAGTX0501_010035-T1 | IPR002922 Thiazole biosynthetic enzyme Thi4 family, IPR027495 Thiamine thiazole synthase, IPR036188 FAD/NAD(P)-binding domain superfamily | FALSE | NA |
| cluster50 | XANPAGTX0501_010040-T1 | NA | TRUE | NA |
| cluster50 | XANPAGTX0501_010044-T1 | IPR002937 Amine oxidase, IPR036188 FAD/NAD(P)-binding domain superfamily | TRUE | NA |
| cluster50 | XANPAGTX0501_010038-T3 | IPR000581 Dihydroxy-acid/6-phosphogluconate dehydratase, IPR004404 Dihydroxy-acid dehydratase, IPR020558 Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site, IPR037237 IlvD/EDD, N-terminal domain, IPR042096 Dihydroxy-acid dehydratase, C-terminal | FALSE | NA |
| cluster50 | XANPAGTX0501_010045-T1 | IPR002937 Amine oxidase, IPR036188 FAD/NAD(P)-binding domain superfamily | FALSE | NA |
| cluster50 | XANPAGTX0501_010039-T1 | NA | FALSE | NA |
| cluster51 | XANPAGTX0501_001936-T1 | NA | FALSE | NA |
| cluster51 | XANPAGTX0501_001926-T1 | NA | FALSE | NA |
| cluster51 | XANPAGTX0501_001921-T1 | IPR025714 Methyltransferase domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR041698 Methyltransferase domain 25 | FALSE | NA |
| cluster51 | XANPAGTX0501_001930-T1 | NA | FALSE | NA |
| cluster51 | XANPAGTX0501_001937-T1 | NA | FALSE | NA |
| cluster51 | XANPAGTX0501_001927-T1 | NA | FALSE | NA |
| cluster51 | XANPAGTX0501_001935-T1 | NA | TRUE | NA |
| cluster52 | XANPAGTX0501_001959-T1 | IPR000095 CRIB domain, IPR000719 Protein kinase domain, IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily, IPR017441 Protein kinase, ATP binding site, IPR033923 p21 activated kinase binding domain, IPR036936 CRIB domain superfamily | FALSE | NA |
| cluster52 | XANPAGTX0501_001967-T1 | NA | FALSE | Cluster_1 |
| cluster52 | XANPAGTX0501_001954-T1 | NA | FALSE | NA |
| cluster52 | XANPAGTX0501_001965-T1 | NA | FALSE | Cluster_1 |
| cluster52 | XANPAGTX0501_001970-T1 | NA | TRUE | Cluster_1 |
| cluster52 | XANPAGTX0501_001963-T1 | NA | FALSE | Cluster_1 |
| cluster52 | XANPAGTX0501_001956-T1 | NA | FALSE | NA |
| cluster52 | XANPAGTX0501_001962-T1 | NA | FALSE | Cluster_1 |
| cluster52 | XANPAGTX0501_001953-T1 | NA | FALSE | NA |
| cluster52 | XANPAGTX0501_001961-T1 | NA | FALSE | Cluster_1 |
| cluster52 | XANPAGTX0501_001966-T1 | NA | FALSE | Cluster_1 |
| cluster52 | XANPAGTX0501_001964-T1 | IPR001611 Leucine-rich repeat, IPR003591 Leucine-rich repeat, typical subtype, IPR019487 RAM signalling pathway, SOG2, IPR032675 Leucine-rich repeat domain superfamily | FALSE | Cluster_1 |
| cluster52 | XANPAGTX0501_001955-T1 | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR001451 Hexapeptide repeat, IPR002110 Ankyrin repeat, IPR011004 Trimeric LpxA-like superfamily, IPR018357 Hexapeptide transferase, conserved site, IPR020683 Domain of unknown function DUF3447, IPR024688 Maltose/galactoside acetyltransferase, IPR036770 Ankyrin repeat-containing domain superfamily, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily | FALSE | NA |
| cluster52 | XANPAGTX0501_001958-T1 | IPR001356 Homeobox domain, IPR009057 Homeobox-like domain superfamily, IPR017970 Homeobox, conserved site | FALSE | NA |
| cluster52 | XANPAGTX0501_001960-T1 | NA | FALSE | Cluster_1 |
| cluster52 | XANPAGTX0501_001957-T1 | NA | FALSE | NA |
| cluster53 | XANPAGTX0501_002182-T1 | NA | FALSE | Cluster_3 |
| cluster53 | XANPAGTX0501_002186-T1 | NA | TRUE | Cluster_3 |
| cluster53 | XANPAGTX0501_002184-T1 | NA | FALSE | Cluster_3 |
| cluster53 | XANPAGTX0501_002190-T1 | IPR001425 Archaeal/bacterial/fungal rhodopsins, IPR018229 Rhodopsin, retinal binding site | FALSE | Cluster_3 |
| cluster53 | XANPAGTX0501_002191-T1 | NA | TRUE | Cluster_3 |
| cluster53 | XANPAGTX0501_002185-T1 | NA | FALSE | Cluster_3 |
| cluster53 | XANPAGTX0501_002183-T1 | NA | FALSE | Cluster_3 |
| cluster54 | XANPAGTX0501_002355-T1 | NA | FALSE | NA |
| cluster54 | XANPAGTX0501_002358-T1 | NA | FALSE | NA |
| cluster54 | XANPAGTX0501_002357-T1 | NA | FALSE | NA |
| cluster54 | XANPAGTX0501_002359-T1 | NA | FALSE | NA |
| cluster54 | XANPAGTX0501_002356-T1 | IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain, IPR029752 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1, IPR029753 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site, IPR036291 NAD(P)-binding domain superfamily | FALSE | NA |
| cluster55 | XANPAGTX0501_002410-T1 | NA | FALSE | NA |
| cluster55 | XANPAGTX0501_002409-T1 | IPR001338 Hydrophobin | TRUE | NA |
| cluster55 | XANPAGTX0501_002412-T2 | NA | TRUE | NA |
| cluster55 | XANPAGTX0501_002411-T1 | NA | FALSE | NA |
| cluster55 | XANPAGTX0501_002412-T1 | NA | TRUE | NA |
| cluster55 | XANPAGTX0501_002408-T1 | NA | FALSE | NA |
| cluster56 | XANPAGTX0501_002441-T1 | NA | FALSE | NA |
| cluster56 | XANPAGTX0501_002437-T1 | IPR001077 O-methyltransferase domain, IPR016461 O-methyltransferase COMT-type, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | NA |
| cluster56 | XANPAGTX0501_002427-T1 | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily | FALSE | NA |
| cluster56 | XANPAGTX0501_002433-T1 | NA | FALSE | NA |
| cluster56 | XANPAGTX0501_002440-T1 | NA | FALSE | NA |
| cluster56 | XANPAGTX0501_002435-T1 | IPR002110 Ankyrin repeat, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster56 | XANPAGTX0501_002428-T1 | NA | FALSE | NA |
| cluster56 | XANPAGTX0501_002434-T1 | IPR002110 Ankyrin repeat, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster56 | XANPAGTX0501_002429-T1 | IPR001077 O-methyltransferase domain, IPR016461 O-methyltransferase COMT-type, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | NA |
| cluster56 | XANPAGTX0501_002436-T1 | IPR002110 Ankyrin repeat, IPR003593 AAA+ ATPase domain, IPR007111 NACHT nucleoside triphosphatase, IPR020683 Domain of unknown function DUF3447, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR031348 Fungal N-terminal domain of STAND protein, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster56 | XANPAGTX0501_002439-T1 | NA | FALSE | NA |
| cluster56 | XANPAGTX0501_002424-T1 | NA | FALSE | NA |
| cluster57 | XANPAGTX0501_010180-T1 | NA | FALSE | NA |
| cluster57 | XANPAGTX0501_010175-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE | NA |
| cluster57 | XANPAGTX0501_010169-T1 | IPR035992 Ricin B-like lectins | FALSE | NA |
| cluster57 | XANPAGTX0501_010173-T1 | NA | FALSE | NA |
| cluster57 | XANPAGTX0501_010171-T1 | NA | FALSE | NA |
| cluster57 | XANPAGTX0501_010172-T1 | IPR010730 Heterokaryon incompatibility | FALSE | NA |
| cluster57 | XANPAGTX0501_010174-T1 | NA | FALSE | NA |
| cluster57 | XANPAGTX0501_010170-T1 | IPR000772 Ricin B, lectin domain, IPR035992 Ricin B-like lectins | TRUE | NA |
| cluster58 | XANPAGTX0501_010244-T1 | IPR000182 GNAT domain, IPR016181 Acyl-CoA N-acyltransferase | FALSE | NA |
| cluster58 | XANPAGTX0501_010248-T1 | IPR000073 Alpha/beta hydrolase fold-1, IPR029058 Alpha/Beta hydrolase fold | FALSE | NA |
| cluster58 | XANPAGTX0501_010247-T1 | NA | TRUE | NA |
| cluster58 | XANPAGTX0501_010250-T1 | NA | TRUE | NA |
| cluster59 | XANPAGTX0501_010478-T1 | IPR000589 Ribosomal protein S15, IPR009068 S15/NS1, RNA-binding | FALSE | NA |
| cluster59 | XANPAGTX0501_010475-T1 | IPR007111 NACHT nucleoside triphosphatase, IPR027417 P-loop containing nucleoside triphosphate hydrolase | FALSE | NA |
| cluster59 | XANPAGTX0501_010476-T1 | NA | FALSE | NA |
| cluster59 | XANPAGTX0501_010479-T1 | NA | FALSE | NA |
| cluster60 | XANPAGTX0501_010557-T1 | IPR000073 Alpha/beta hydrolase fold-1, IPR022742 Serine aminopeptidase, S33, IPR029058 Alpha/Beta hydrolase fold | FALSE | NA |
| cluster60 | XANPAGTX0501_010558-T1 | IPR000719 Protein kinase domain, IPR008266 Tyrosine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily, IPR017441 Protein kinase, ATP binding site | FALSE | NA |
| cluster60 | XANPAGTX0501_010559-T1 | NA | FALSE | NA |
| cluster60 | XANPAGTX0501_010556-T1 | IPR000719 Protein kinase domain, IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily | FALSE | NA |
| cluster60 | XANPAGTX0501_010551-T1 | IPR006094 FAD linked oxidase, N-terminal, IPR016166 FAD-binding domain, PCMH-type, IPR016169 FAD-binding, type PCMH, subdomain 2, IPR036318 FAD-binding, type PCMH-like superfamily | FALSE | NA |
| cluster60 | XANPAGTX0501_010552-T1 | NA | FALSE | NA |
| cluster61 | XANPAGTX0501_010572-T1 | NA | FALSE | NA |
| cluster61 | XANPAGTX0501_010571-T1 | IPR029498 Prion-inhibition and propagation, HeLo domain, IPR038305 HeLo domain superfamily | FALSE | NA |
| cluster61 | XANPAGTX0501_010570-T1 | IPR002182 NB-ARC, IPR010730 Heterokaryon incompatibility, IPR011990 Tetratricopeptide-like helical domain superfamily, IPR013026 None, IPR019734 Tetratricopeptide repeat, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR031352 NACHT-NTPase and P-loop NTPases, N-terminal domain, IPR041664 Orc1-like, AAA ATPase domain | FALSE | NA |
| cluster62 | XANPAGTX0501_002486-T1 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | FALSE | Cluster_2 |
| cluster62 | XANPAGTX0501_002483-T3 | IPR007229 Nicotinate phosphoribosyltransferase family, IPR036068 Nicotinate phosphoribosyltransferase-like, C-terminal, IPR040727 Nicotinate phosphoribosyltransferase, N-terminal domain, IPR041525 Nicotinate/nicotinamide phosphoribosyltransferase | FALSE | Cluster_2 |
| cluster62 | XANPAGTX0501_002491-T1 | IPR021848 Haem-dependent oxidative N-demethylase, alpha subunit-like | FALSE | Cluster_2 |
| cluster62 | XANPAGTX0501_002488-T1 | IPR000873 AMP-dependent synthetase/ligase domain, IPR009081 Phosphopantetheine binding ACP domain, IPR010071 Amino acid adenylation domain, IPR010080 Thioester reductase-like domain, IPR013120 Fatty acyl-coenzyme A reductase, NAD-binding domain, IPR020845 AMP-binding, conserved site, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR042099 ANL, N-terminal domain | FALSE | Cluster_2 |
| cluster62 | XANPAGTX0501_002487-T1 | IPR001585 Transaldolase/Fructose-6-phosphate aldolase, IPR013785 Aldolase-type TIM barrel, IPR018225 Transaldolase, active site | FALSE | Cluster_2 |
| cluster62 | XANPAGTX0501_002490-T1 | IPR036291 NAD(P)-binding domain superfamily | FALSE | Cluster_2 |
| cluster63 | XANPAGTX0501_002503-T1 | NA | FALSE | NA |
| cluster63 | XANPAGTX0501_002505-T1 | NA | FALSE | NA |
| cluster63 | XANPAGTX0501_002504-T1 | IPR008441 AfumC-like glycosyltransferase, IPR029044 Nucleotide-diphospho-sugar transferases | FALSE | NA |
| cluster63 | XANPAGTX0501_002506-T1 | NA | FALSE | NA |
| cluster63 | XANPAGTX0501_002514-T1 | NA | TRUE | NA |
| cluster64 | XANPAGTX0501_002562-T1 | IPR004045 Glutathione S-transferase, N-terminal, IPR004046 Glutathione S-transferase, C-terminal, IPR010987 Glutathione S-transferase, C-terminal-like, IPR036249 Thioredoxin-like superfamily, IPR036282 Glutathione S-transferase, C-terminal domain superfamily, IPR040079 Glutathione transferase family | FALSE | NA |
| cluster64 | XANPAGTX0501_002566-T1 | IPR002893 Zinc finger, MYND-type, IPR027974 Domain of unknown function DUF4470 | FALSE | NA |
| cluster64 | XANPAGTX0501_002565-T1 | NA | TRUE | NA |
| cluster65 | XANPAGTX0501_002780-T1 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | FALSE | NA |
| cluster65 | XANPAGTX0501_002783-T1 | NA | FALSE | NA |
| cluster65 | XANPAGTX0501_002791-T1 | IPR024079 Metallopeptidase, catalytic domain superfamily | FALSE | NA |
| cluster65 | XANPAGTX0501_002792-T1 | NA | FALSE | NA |
| cluster66 | XANPAGTX0501_002946-T1 | NA | FALSE | NA |
| cluster66 | XANPAGTX0501_002943-T1 | NA | FALSE | NA |
| cluster66 | XANPAGTX0501_002947-T1 | IPR000330 SNF2, N-terminal, IPR001650 Helicase, C-terminal, IPR001841 Zinc finger, RING-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR014001 Helicase superfamily 1/2, ATP-binding domain, IPR017907 Zinc finger, RING-type, conserved site, IPR018957 Zinc finger, C3HC4 RING-type, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR038718 SNF2-like, N-terminal domain superfamily | FALSE | NA |
| cluster67 | XANPAGTX0501_002961-T1 | NA | FALSE | NA |
| cluster67 | XANPAGTX0501_002962-T1 | NA | FALSE | NA |
| cluster67 | XANPAGTX0501_002967-T1 | NA | FALSE | NA |
| cluster68 | XANPAGTX0501_010596-T1 | NA | FALSE | NA |
| cluster68 | XANPAGTX0501_010597-T1 | NA | FALSE | NA |
| cluster68 | XANPAGTX0501_010598-T1 | NA | FALSE | NA |
| cluster68 | XANPAGTX0501_010603-T1 | NA | FALSE | NA |
| cluster68 | XANPAGTX0501_010604-T1 | IPR002110 Ankyrin repeat, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster68 | XANPAGTX0501_010605-T1 | IPR002110 Ankyrin repeat, IPR020683 Domain of unknown function DUF3447, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster68 | XANPAGTX0501_010606-T1 | IPR002110 Ankyrin repeat, IPR020683 Domain of unknown function DUF3447, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster68 | XANPAGTX0501_010607-T1 | IPR002110 Ankyrin repeat, IPR003593 AAA+ ATPase domain, IPR007111 NACHT nucleoside triphosphatase, IPR020683 Domain of unknown function DUF3447, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR031348 Fungal N-terminal domain of STAND protein, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster68 | XANPAGTX0501_010608-T1 | IPR002110 Ankyrin repeat, IPR003593 AAA+ ATPase domain, IPR007111 NACHT nucleoside triphosphatase, IPR020683 Domain of unknown function DUF3447, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR031348 Fungal N-terminal domain of STAND protein, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster69 | XANPAGTX0501_003173-T1 | NA | FALSE | Cluster_1 |
| cluster69 | XANPAGTX0501_003171-T1 | NA | FALSE | Cluster_1 |
| cluster69 | XANPAGTX0501_003172-T1 | NA | FALSE | Cluster_1 |
| cluster70 | XANPAGTX0501_003213-T1 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | FALSE | NA |
| cluster70 | XANPAGTX0501_003198-T1 | IPR022085 Oxopyrrolidines biosynthesis cluster protein G | FALSE | Cluster_2 |
| cluster70 | XANPAGTX0501_003205-T1 | IPR001128 Cytochrome P450, IPR002401 Cytochrome P450, E-class, group I, IPR017972 Cytochrome P450, conserved site, IPR036396 Cytochrome P450 superfamily | FALSE | NA |
| cluster70 | XANPAGTX0501_003212-T1 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | FALSE | NA |
| cluster70 | XANPAGTX0501_003200-T1 | NA | FALSE | Cluster_2 |
| cluster70 | XANPAGTX0501_003211-T1 | NA | FALSE | NA |
| cluster70 | XANPAGTX0501_003199-T1 | IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily, IPR039559 Altered inheritance of mitochondria protein 6, PI-PLC-like catalytic domain | FALSE | Cluster_2 |
| cluster71 | XANPAGTX0501_003289-T1 | NA | FALSE | Cluster_4 |
| cluster71 | XANPAGTX0501_003282-T1 | NA | FALSE | NA |
| cluster71 | XANPAGTX0501_003283-T1 | NA | FALSE | NA |
| cluster71 | XANPAGTX0501_003285-T1 | IPR008758 Peptidase S28, IPR029058 Alpha/Beta hydrolase fold, IPR042269 Serine carboxypeptidase S28, SKS domain | TRUE | NA |
| cluster71 | XANPAGTX0501_003287-T1 | NA | TRUE | Cluster_4 |
| cluster72 | XANPAGTX0501_003714-T1 | IPR001077 O-methyltransferase domain, IPR016461 O-methyltransferase COMT-type, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR036388 Winged helix-like DNA-binding domain superfamily, IPR036390 Winged helix DNA-binding domain superfamily | FALSE | NA |
| cluster72 | XANPAGTX0501_003715-T1 | NA | FALSE | NA |
| cluster72 | XANPAGTX0501_003723-T1 | NA | FALSE | NA |
| cluster73 | XANPAGTX0501_003766-T1 | NA | TRUE | NA |
| cluster73 | XANPAGTX0501_003775-T2 | IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily | FALSE | NA |
| cluster73 | XANPAGTX0501_003775-T1 | IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily | FALSE | NA |
| cluster73 | XANPAGTX0501_003767-T1 | NA | FALSE | NA |
| cluster73 | XANPAGTX0501_003765-T1 | IPR000420 Yeast PIR protein repeat | TRUE | NA |
| cluster74 | XANPAGTX0501_004003-T1 | NA | FALSE | NA |
| cluster74 | XANPAGTX0501_004008-T1 | NA | FALSE | NA |
| cluster74 | XANPAGTX0501_004006-T1 | IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR041677 DNA2/NAM7 helicase, helicase domain, IPR041679 DNA2/NAM7 helicase-like, C-terminal | FALSE | NA |
| cluster75 | XANPAGTX0501_004414-T1 | IPR027417 P-loop containing nucleoside triphosphate hydrolase | FALSE | Cluster_2 |
| cluster75 | XANPAGTX0501_004416-T1 | IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1 | FALSE | Cluster_2 |
| cluster75 | XANPAGTX0501_004407-T1 | IPR002925 Dienelactone hydrolase, IPR029058 Alpha/Beta hydrolase fold | FALSE | Cluster_2 |
| cluster75 | XANPAGTX0501_004415-T1 | NA | FALSE | Cluster_2 |
| cluster76 | XANPAGTX0501_004429-T1 | NA | FALSE | NA |
| cluster76 | XANPAGTX0501_004431-T1 | NA | FALSE | NA |
| cluster76 | XANPAGTX0501_004430-T1 | NA | FALSE | NA |
| cluster76 | XANPAGTX0501_004428-T1 | IPR004695 Transporter protein SLAC1/Mae1/ Ssu1/TehA, IPR030185 Malic acid transport protein, IPR038665 Voltage-dependent anion channel superfamily | FALSE | NA |
| cluster77 | XANPAGTX0501_004520-T1 | NA | FALSE | NA |
| cluster77 | XANPAGTX0501_004519-T1 | NA | FALSE | NA |
| cluster77 | XANPAGTX0501_004521-T1 | IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily | FALSE | NA |
| cluster77 | XANPAGTX0501_004530-T1 | NA | FALSE | NA |
| cluster77 | XANPAGTX0501_004515-T1 | IPR032710 NTF2-like domain superfamily, IPR037401 SnoaL-like domain | TRUE | NA |
| cluster77 | XANPAGTX0501_004525-T1 | IPR000719 Protein kinase domain, IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily | FALSE | NA |
| cluster78 | XANPAGTX0501_004956-T1 | NA | TRUE | NA |
| cluster78 | XANPAGTX0501_004961-T1 | IPR002110 Ankyrin repeat, IPR020683 Domain of unknown function DUF3447, IPR031348 Fungal N-terminal domain of STAND protein, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster78 | XANPAGTX0501_004963-T1 | IPR001915 Peptidase M48 | FALSE | NA |
| cluster78 | XANPAGTX0501_004965-T1 | NA | FALSE | NA |
| cluster78 | XANPAGTX0501_004966-T1 | NA | FALSE | NA |
| cluster79 | XANPAGTX0501_004998-T1 | IPR000182 GNAT domain, IPR016181 Acyl-CoA N-acyltransferase | FALSE | NA |
| cluster79 | XANPAGTX0501_004997-T1 | NA | FALSE | NA |
| cluster79 | XANPAGTX0501_004983-T1 | NA | TRUE | NA |
| cluster79 | XANPAGTX0501_004996-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE | NA |
| cluster79 | XANPAGTX0501_004991-T1 | NA | FALSE | NA |
| cluster79 | XANPAGTX0501_004992-T1 | IPR013087 Zinc finger C2H2-type | FALSE | NA |
| cluster79 | XANPAGTX0501_004990-T1 | NA | FALSE | NA |
| cluster80 | XANPAGTX0501_005026-T1 | NA | FALSE | NA |
| cluster80 | XANPAGTX0501_005021-T1 | NA | FALSE | NA |
| cluster80 | XANPAGTX0501_005022-T1 | NA | FALSE | NA |
| cluster80 | XANPAGTX0501_005029-T1 | NA | FALSE | NA |
| cluster80 | XANPAGTX0501_005027-T1 | IPR003370 Chromate transporter, IPR014047 Chromate transporter, long chain | FALSE | NA |
| cluster80 | XANPAGTX0501_005033-T1 | NA | FALSE | NA |
| cluster80 | XANPAGTX0501_005028-T1 | NA | FALSE | NA |
| cluster80 | XANPAGTX0501_005025-T1 | NA | FALSE | NA |
| cluster81 | XANPAGTX0501_005082-T1 | IPR000537 UbiA prenyltransferase family | FALSE | Cluster_3 |
| cluster81 | XANPAGTX0501_005081-T1 | NA | FALSE | Cluster_3 |
| cluster81 | XANPAGTX0501_005084-T1 | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR036318 FAD-binding, type PCMH-like superfamily | FALSE | Cluster_3 |
| cluster81 | XANPAGTX0501_005085-T1 | NA | FALSE | Cluster_3 |
| cluster81 | XANPAGTX0501_005076-T1 | IPR000092 Polyprenyl synthetase, IPR008949 Isoprenoid synthase domain superfamily, IPR033749 Polyprenyl synthetase, conserved site | FALSE | Cluster_3 |
| cluster81 | XANPAGTX0501_005074-T1 | NA | FALSE | Cluster_3 |
| cluster81 | XANPAGTX0501_005083-T1 | IPR000073 Alpha/beta hydrolase fold-1, IPR029058 Alpha/Beta hydrolase fold | FALSE | Cluster_3 |
| cluster82 | XANPAGTX0501_005252-T1 | IPR001227 Acyl transferase domain superfamily, IPR009081 Phosphopantetheine binding ACP domain, IPR013217 Methyltransferase type 12, IPR013968 Polyketide synthase, ketoreductase domain, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016036 Malonyl-CoA ACP transacylase, ACP-binding, IPR016039 Thiolase-like, IPR018201 Beta-ketoacyl synthase, active site, IPR020801 None, IPR020806 Polyketide synthase, phosphopantetheine-binding domain, IPR020807 Polyketide synthase, dehydratase domain, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR032821 Polyketide synthase, C-terminal extension, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR042104 Polyketide synthase, dehydratase domain superfamily | FALSE | Cluster_2 |
| cluster82 | XANPAGTX0501_005256-T1 | IPR006094 FAD linked oxidase, N-terminal, IPR012951 Berberine/berberine-like, IPR016166 FAD-binding domain, PCMH-type, IPR036318 FAD-binding, type PCMH-like superfamily | TRUE | Cluster_2 |
| cluster82 | XANPAGTX0501_005254-T1 | IPR007527 Zinc finger, SWIM-type | FALSE | Cluster_2 |
| cluster82 | XANPAGTX0501_005265-T1 | IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR035940 CAP superfamily | FALSE | Cluster_2 |
| cluster82 | XANPAGTX0501_005255-T1 | IPR016040 NAD(P)-binding domain, IPR036291 NAD(P)-binding domain superfamily | FALSE | Cluster_2 |
| cluster82 | XANPAGTX0501_005253-T1 | IPR005123 Oxoglutarate/iron-dependent dioxygenase, IPR027443 Isopenicillin N synthase-like superfamily | FALSE | Cluster_2 |
| cluster83 | XANPAGTX0501_005280-T1 | NA | FALSE | Cluster_3 |
| cluster83 | XANPAGTX0501_005278-T1 | NA | FALSE | NA |
| cluster83 | XANPAGTX0501_005281-T1 | NA | FALSE | Cluster_3 |
| cluster83 | XANPAGTX0501_005284-T1 | NA | FALSE | Cluster_3 |
| cluster83 | XANPAGTX0501_005271-T1 | NA | FALSE | NA |
| cluster83 | XANPAGTX0501_005279-T1 | NA | FALSE | Cluster_3 |
| cluster84 | XANPAGTX0501_005361-T1 | NA | TRUE | Cluster_4 |
| cluster84 | XANPAGTX0501_005362-T1 | NA | FALSE | Cluster_4 |
| cluster84 | XANPAGTX0501_005378-T1 | IPR002293 Amino acid/polyamine transporter I | FALSE | Cluster_5 |
| cluster84 | XANPAGTX0501_005364-T1 | NA | TRUE | NA |
| cluster84 | XANPAGTX0501_005371-T1 | NA | FALSE | NA |
| cluster84 | XANPAGTX0501_005367-T1 | NA | FALSE | NA |
| cluster84 | XANPAGTX0501_005368-T1 | NA | FALSE | NA |
| cluster84 | XANPAGTX0501_005370-T1 | NA | FALSE | NA |
| cluster85 | XANPAGTX0501_005534-T1 | NA | FALSE | NA |
| cluster85 | XANPAGTX0501_005531-T1 | IPR008949 Isoprenoid synthase domain superfamily | FALSE | NA |
| cluster85 | XANPAGTX0501_005529-T1 | IPR002110 Ankyrin repeat, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster85 | XANPAGTX0501_005532-T1 | IPR008949 Isoprenoid synthase domain superfamily | FALSE | NA |
| cluster85 | XANPAGTX0501_005530-T1 | IPR008949 Isoprenoid synthase domain superfamily | FALSE | NA |
| cluster85 | XANPAGTX0501_005541-T1 | NA | FALSE | NA |
| cluster85 | XANPAGTX0501_005533-T1 | NA | TRUE | NA |
| cluster86 | XANPAGTX0501_005615-T1 | NA | FALSE | NA |
| cluster86 | XANPAGTX0501_005613-T1 | IPR003615 HNH nuclease | FALSE | NA |
| cluster86 | XANPAGTX0501_005602-T1 | IPR000073 Alpha/beta hydrolase fold-1, IPR000639 Epoxide hydrolase-like, IPR029058 Alpha/Beta hydrolase fold | FALSE | NA |
| cluster86 | XANPAGTX0501_005610-T1 | NA | FALSE | NA |
| cluster86 | XANPAGTX0501_005604-T1 | IPR015590 Aldehyde dehydrogenase domain, IPR016161 Aldehyde/histidinol dehydrogenase, IPR016162 Aldehyde dehydrogenase, N-terminal, IPR016163 Aldehyde dehydrogenase, C-terminal, IPR029510 Aldehyde dehydrogenase, glutamic acid active site | FALSE | NA |
| cluster86 | XANPAGTX0501_005612-T1 | NA | FALSE | NA |
| cluster86 | XANPAGTX0501_005611-T1 | NA | FALSE | NA |
| cluster86 | XANPAGTX0501_005614-T1 | NA | FALSE | NA |
| cluster87 | XANPAGTX0501_005697-T2 | IPR002110 Ankyrin repeat, IPR003593 AAA+ ATPase domain, IPR007111 NACHT nucleoside triphosphatase, IPR020683 Domain of unknown function DUF3447, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR031348 Fungal N-terminal domain of STAND protein, IPR036770 Ankyrin repeat-containing domain superfamily | FALSE | NA |
| cluster87 | XANPAGTX0501_005693-T1 | NA | FALSE | NA |
| cluster87 | XANPAGTX0501_005695-T1 | NA | FALSE | NA |
| cluster87 | XANPAGTX0501_005694-T1 | NA | FALSE | NA |
| cluster87 | XANPAGTX0501_005692-T1 | IPR000873 AMP-dependent synthetase/ligase domain, IPR009081 Phosphopantetheine binding ACP domain, IPR010071 Amino acid adenylation domain, IPR010080 Thioester reductase-like domain, IPR013120 Fatty acyl-coenzyme A reductase, NAD-binding domain, IPR020845 AMP-binding, conserved site, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR042099 ANL, N-terminal domain | FALSE | NA |
| cluster87 | XANPAGTX0501_005699-T1 | IPR010730 Heterokaryon incompatibility | FALSE | NA |
| cluster88 | XANPAGTX0501_005737-T1 | IPR002347 Short-chain dehydrogenase/reductase SDR, IPR036291 NAD(P)-binding domain superfamily | FALSE | Cluster_1 |
| cluster88 | XANPAGTX0501_005733-T1 | NA | TRUE | Cluster_1 |
| cluster88 | XANPAGTX0501_005735-T1 | IPR018824 Conidiation-specific protein 6 | FALSE | Cluster_1 |
| cluster88 | XANPAGTX0501_005732-T1 | IPR001128 Cytochrome P450, IPR002401 Cytochrome P450, E-class, group I, IPR017972 Cytochrome P450, conserved site, IPR036396 Cytochrome P450 superfamily | FALSE | Cluster_1 |
| cluster89 | XANPAGTX0501_005775-T1 | NA | FALSE | NA |
| cluster89 | XANPAGTX0501_005766-T1 | NA | FALSE | NA |
| cluster89 | XANPAGTX0501_005770-T1 | IPR002347 Short-chain dehydrogenase/reductase SDR, IPR036291 NAD(P)-binding domain superfamily | FALSE | NA |
| cluster89 | XANPAGTX0501_005771-T1 | IPR001547 Glycoside hydrolase, family 5, IPR017853 Glycoside hydrolase superfamily | TRUE | NA |
| cluster90 | XANPAGTX0501_006137-T1 | NA | FALSE | NA |
| cluster90 | XANPAGTX0501_006141-T1 | NA | FALSE | NA |
| cluster90 | XANPAGTX0501_006142-T1 | NA | TRUE | NA |
| cluster90 | XANPAGTX0501_006143-T1 | NA | FALSE | NA |
| cluster91 | XANPAGTX0501_006205-T1 | NA | FALSE | NA |
| cluster91 | XANPAGTX0501_006203-T1 | IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site | FALSE | NA |
| cluster91 | XANPAGTX0501_006215-T1 | NA | FALSE | NA |
| cluster91 | XANPAGTX0501_006214-T1 | NA | FALSE | NA |
| cluster91 | XANPAGTX0501_006204-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006245-T1 | NA | TRUE | NA |
| cluster92 | XANPAGTX0501_006239-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006250-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006243-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006256-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006232-T1 | IPR002347 Short-chain dehydrogenase/reductase SDR, IPR036291 NAD(P)-binding domain superfamily | FALSE | NA |
| cluster92 | XANPAGTX0501_006255-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006233-T1 | IPR001128 Cytochrome P450, IPR002403 Cytochrome P450, E-class, group IV, IPR036396 Cytochrome P450 superfamily | FALSE | NA |
| cluster92 | XANPAGTX0501_006262-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006253-T1 | IPR014849 EKC/KEOPS complex, subunit Gon7 | FALSE | NA |
| cluster92 | XANPAGTX0501_006257-T1 | IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily | TRUE | NA |
| cluster92 | XANPAGTX0501_006238-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006246-T1 | NA | FALSE | NA |
| cluster92 | XANPAGTX0501_006237-T1 | IPR002347 Short-chain dehydrogenase/reductase SDR, IPR036291 NAD(P)-binding domain superfamily | FALSE | NA |
croc_c<-read.delim("../analysis_and_temp_files/08_dge_culture_lichen/croc_culture_upregulated.txt",header=F)
croc_c$cluster<-paste0("cluster",1:nrow(croc_c))
croc_c<-croc_c %>% separate_longer_delim(V9, delim = " ") %>% filter(V9!="") %>%
select(-c(V7,V8,V2,V3))
colnames(croc_c)<-c("contig","start","end","pval","TranscriptID","cluster")
croc_c %>% group_by(cluster) %>% summarize(n=n()) %>% arrange(desc(n)) %>% head()
## # A tibble: 6 × 2
## cluster n
## <chr> <int>
## 1 cluster31 13
## 2 cluster22 10
## 3 cluster27 10
## 4 cluster38 10
## 5 cluster39 9
## 6 cluster43 9
croc_l3<-croc_l2 %>%
mutate(is_SM = ifelse(is.na(antiSMASH),"not_in_SM_cluster","in_SM_cluster")) %>%
group_by(cluster,is_SM) %>% summarize(n=n()) %>%
pivot_wider(values_from = n, values_fill = 0, names_from = is_SM)
## `summarise()` has grouped output by 'cluster'. You can override using the
## `.groups` argument.
croc_c2<-croc_c %>% left_join(funannot2) %>%
select(cluster,antiSMASH,TranscriptID, InterPro_new,secreted_consensus)
## Joining with `by = join_by(TranscriptID)`
croc_c3<-croc_c2 %>%
mutate(is_SM = ifelse(is.na(antiSMASH),"not_in_SM_cluster","in_SM_cluster")) %>%
group_by(cluster,is_SM) %>% summarize(n=n()) %>%
pivot_wider(values_from = n, values_fill = 0, names_from = is_SM)
## `summarise()` has grouped output by 'cluster'. You can override using the
## `.groups` argument.
#First, save CROC tables in a bed format
croc_l<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/croc_lichen_upregulated.txt",header=F)
write.table(croc_l[,c(1,4,5)],"../analysis_and_temp_files/08_dge_culture_lichen/GTX0501_lichen_upregulated_croc.bed",col.names = F,row.names = F,quote = F,sep="\t")
croc_c<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/croc_culture_upregulated.txt",header=F)
write.table(croc_c[,c(1,4,5)],"../analysis_and_temp_files/08_dge_culture_lichen/GTX0501_culture_upregulated_croc.bed",col.names = F,row.names = F,quote = F,sep="\t")
#intersec CROC file with the bed file
sbatch --mem=10G -c 5 --partition=tsl-short --wrap="source package b0ed0698-358b-4c9b-9d21-603ea8d6e478; bedtools coverage -a ../02_mycobiont_genome/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_xanthoria_nuclear_mag_clean_sort.bed -b analysis_and_temp_files/08_dge_culture_lichen/GTX0501_lichen_upregulated_croc.bed > analysis_and_temp_files/08_dge_culture_lichen/GTX0501_xanthoria_nuclear_mag_clean_sort_lichen_upregulated_croc_bedtools.txt"
sbatch --mem=10G -c 5 --partition=tsl-short --wrap="source package b0ed0698-358b-4c9b-9d21-603ea8d6e478; bedtools coverage -a ../02_mycobiont_genome/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_xanthoria_nuclear_mag_clean_sort.bed -b analysis_and_temp_files/08_dge_culture_lichen/GTX0501_culture_upregulated_croc.bed > analysis_and_temp_files/08_dge_culture_lichen/GTX0501_xanthoria_nuclear_mag_clean_sort_culture_upregulated_croc_bedtools.txt"
#read in separately
croc_l<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/GTX0501_xanthoria_nuclear_mag_clean_sort_lichen_upregulated_croc_bedtools.txt",header=F)[,c(1,2,7)]
colnames(croc_l)<-c("contig","window_start","croc")
croc_l$croc<-as.numeric(croc_l$croc)
croc_l<-croc_l %>% mutate(croc_binary_l=if_else(croc>0,1,0))
croc_c<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/GTX0501_xanthoria_nuclear_mag_clean_sort_culture_upregulated_croc_bedtools.txt",header=F)[,c(1,2,7)]
colnames(croc_c)<-c("contig","window_start","croc")
croc_c$croc<-as.numeric(croc_c$croc)
croc_c<-croc_c %>% mutate(croc_binary_c=if_else(croc>0,1,0))
ggplot(croc_l,aes(y=fct_reorder(contig,window_start),x=window_start))+
geom_tile(aes(height=0.1),fill="black")+
geom_tile(aes(fill=croc_binary_l,alpha=croc_binary_l))+
xlab("")+ylab("")+
scale_alpha_continuous(range=c(0,1))+
scale_fill_gradient(low="#f0f0f0",high="#F8766D")+
scale_x_continuous(breaks = c(0,1000000,2000000,3000000,4000000),
labels = c("0","1 Mbp","2 Mbp","3 Mbp","4 Mbp"))+
theme_minimal()+
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
* Plot culture upregulated
ggplot(croc_c,aes(y=fct_reorder(contig,window_start),x=window_start))+
geom_tile(aes(height=0.1),fill="black")+
geom_tile(aes(fill=croc_binary_c,alpha=croc_binary_c))+
xlab("")+ylab("")+
scale_alpha_continuous(range=c(0,1))+
scale_fill_gradient(low="#f0f0f0",high="#619CFF")+
scale_x_continuous(breaks = c(0,1000000,2000000,3000000,4000000),
labels = c("0","1 Mbp","2 Mbp","3 Mbp","4 Mbp"))+
theme_minimal()+
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
library(ggnewscale)
library(patchwork)
rep<-read.delim2("../../02_mycobiont_genome/analysis_and_temp_files/06_annotate_lecanoro/GTX0501_xanthoria_nuclear_mag_clean_sort_repeatcov.txt",header=F)[,c(1,2,7)]
colnames(rep)<-c("contig","window_start","repeat_content")
rep$repeat_content<- rep$repeat_content %>% as.numeric()
df2 <- rep %>% left_join(croc_l %>% select(-croc)) %>%
left_join(croc_c %>% select(-croc)) %>%
pivot_longer(-c(contig, window_start),names_to = "parameter",values_to = "value")
## Joining with `by = join_by(contig, window_start)`
## Joining with `by = join_by(contig, window_start)`
df2$parameter<-plyr::revalue(df2$parameter, c( "repeat_content"="CRepeat%","croc_binary_l"="BLichen_upregulated",
"croc_binary_c"="ACulture_upregulated"))
df2$contig<-reorder(df2$contig,df2$contig,FUN=function(x) -length(x))
df2<-df2 %>% mutate(panel=case_when(
contig %in% c("Xp_GTX0501_1","Xp_GTX0501_2","Xp_GTX0501_3", "Xp_GTX0501_4",
"Xp_GTX0501_5", "Xp_GTX0501_6", "Xp_GTX0501_7", "Xp_GTX0501_8",
"Xp_GTX0501_9", "Xp_GTX0501_10", "Xp_GTX0501_11", "Xp_GTX0501_12",
"Xp_GTX0501_13", "Xp_GTX0501_14", "Xp_GTX0501_15", "Xp_GTX0501_16",
"Xp_GTX0501_17", "Xp_GTX0501_18", "Xp_GTX0501_19") ~ 1,
contig %in% c("Xp_GTX0501_19", "Xp_GTX0501_20","Xp_GTX0501_21", "Xp_GTX0501_22", "Xp_GTX0501_23", "Xp_GTX0501_24","Xp_GTX0501_25", "Xp_GTX0501_26", "Xp_GTX0501_27", "Xp_GTX0501_28","Xp_GTX0501_29", "Xp_GTX0501_30", "Xp_GTX0501_31", "Xp_GTX0501_32",
"Xp_GTX0501_33", "Xp_GTX0501_34", "Xp_GTX0501_35", "Xp_GTX0501_36", "Xp_GTX0501_37", "Xp_GTX0501_38") ~ 2, T ~3))
gg1<-df2 %>% filter(panel==1) |>
ggplot() +
# apply the gradient to group 1
geom_tile(aes(y=parameter,x=window_start,fill=value),
filter(df2, parameter == "CRepeat%",panel==1)) +
scale_fill_gradientn(colours = c("purple", "orange"),guide = 'none')+
labs(fill = "Repeat%") +
# start a new scale
new_scale_fill() +
geom_tile(aes(y=parameter,x=window_start,height=0.25),fill="black", filter(df2, parameter == "BLichen_upregulated",panel==1))+
geom_tile(aes(y=parameter,x=window_start,fill=value,alpha=value), filter(df2, parameter == "BLichen_upregulated",panel==1))+
scale_alpha_continuous(range=c(0,1),guide = 'none')+
scale_fill_gradientn(colours = c("white","#F8766D"),guide = 'none')+
# start a new scale
new_scale_fill() +
geom_tile(aes(y=parameter,x=window_start,height=0.25),fill="black", filter(df2, parameter == "ACulture_upregulated",panel==1))+
geom_tile(aes(y=parameter,x=window_start,fill=value,alpha=value), filter(df2, parameter == "ACulture_upregulated",panel==1))+
scale_alpha_continuous(range=c(0,1),guide = 'none')+
scale_fill_gradientn(colours = c("white","#619CFF"),guide = 'none')+
scale_x_continuous(breaks = c(0,1000000,2000000,3000000,4000000),
labels = c("0","1 Mbp","2 Mbp","3 Mbp","4 Mbp"),expand = c(0, 0))+
labs(fill = "Culture-upregulated clusters") + xlab("")+ylab("Contigs")+
facet_wrap(~contig,ncol=1)+
theme_classic()+
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
strip.background = element_blank(),strip.text.x = element_blank(),
axis.text.y = element_blank(),legend.position="bottom",
axis.line.y = element_blank(),axis.ticks.y = element_blank())
## Scale for alpha is already present.
## Adding another scale for alpha, which will replace the existing scale.
gg2<-df2 %>% filter(panel==2) |>
ggplot() +
# apply the gradient to group 1
geom_tile(aes(y=parameter,x=window_start,fill=value),
filter(df2, parameter == "CRepeat%",panel==2)) +
scale_fill_gradientn(colours = c("purple", "orange"),guide = 'none')+
labs(fill = "Repeat%") +
# start a new scale
new_scale_fill() +
geom_tile(aes(y=parameter,x=window_start,height=0.25),fill="black", filter(df2, parameter == "BLichen_upregulated",panel==2))+
geom_tile(aes(y=parameter,x=window_start,fill=value,alpha=value), filter(df2, parameter == "BLichen_upregulated",panel==2))+
scale_alpha_continuous(range=c(0,1),guide = 'none')+
scale_fill_gradientn(colours = c("white","#F8766D"),guide = 'none')+
# start a new scale
new_scale_fill() +
geom_tile(aes(y=parameter,x=window_start,height=0.25),fill="black", filter(df2, parameter == "ACulture_upregulated",panel==2))+
geom_tile(aes(y=parameter,x=window_start,fill=value,alpha=value), filter(df2, parameter == "ACulture_upregulated",panel==2))+
scale_alpha_continuous(range=c(0,1),guide = 'none')+
scale_fill_gradientn(colours = c("white","#619CFF"),guide = 'none')+
scale_x_continuous(breaks = c(0,1000000,2000000,3000000,4000000),
labels = c("0","1 Mbp","2 Mbp","3 Mbp","4 Mbp"),expand = c(0, 0))+
labs(fill = "Culture-upregulated clusters") + xlab("")+ylab("Contigs")+
facet_wrap(~contig,ncol=1)+
theme_classic()+
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
strip.background = element_blank(),strip.text.x = element_blank(),
axis.text.y = element_blank(),legend.position="bottom",
axis.line.y = element_blank(),axis.ticks.y = element_blank())
## Scale for alpha is already present.
## Adding another scale for alpha, which will replace the existing scale.
gg3<-df2 %>% filter(panel==3) |>
ggplot() +
# apply the gradient to group 1
geom_tile(aes(y=parameter,x=window_start,fill=value),
filter(df2, parameter == "CRepeat%",panel==3)) +
scale_fill_gradientn(colours = c("purple", "orange"),guide = 'none')+
labs(fill = "Repeat%") +
# start a new scale
new_scale_fill() +
geom_tile(aes(y=parameter,x=window_start,height=0.25),fill="black", filter(df2, parameter == "BLichen_upregulated",panel==3))+
geom_tile(aes(y=parameter,x=window_start,fill=value,alpha=value), filter(df2, parameter == "BLichen_upregulated",panel==3))+
scale_alpha_continuous(range=c(0,1),guide = 'none')+
scale_fill_gradientn(colours = c("white","#F8766D"),guide = 'none')+
# start a new scale
new_scale_fill() +
geom_tile(aes(y=parameter,x=window_start,height=0.25),fill="black", filter(df2, parameter == "ACulture_upregulated",panel==3))+
geom_tile(aes(y=parameter,x=window_start,fill=value,alpha=value), filter(df2, parameter == "ACulture_upregulated",panel==3))+
scale_alpha_continuous(range=c(0,1),guide = 'none')+
scale_fill_gradientn(colours = c("white","#619CFF"),guide = 'none')+
scale_x_continuous(breaks = c(0,1000000,2000000,3000000,4000000),
labels = c("0","1 Mbp","2 Mbp","3 Mbp","4 Mbp"),expand = c(0, 0))+
labs(fill = "Culture-upregulated clusters") + xlab("")+ylab("Contigs")+
facet_wrap(~contig,ncol=1)+
theme_classic()+
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
strip.background = element_blank(),strip.text.x = element_blank(),
axis.text.y = element_blank(),legend.position="bottom",
axis.line.y = element_blank(),axis.ticks.y = element_blank())
## Scale for alpha is already present.
## Adding another scale for alpha, which will replace the existing scale.
#scale graph widths
#max(df$window_start[df$panel==1]) / max(df$window_start[df$panel==3]) [1] 29.44444
#max(df$window_start[df$panel==2]) / max(df$window_start[df$panel==3]) [1] 3.666667
gg1+gg2+gg3 + plot_layout(guides = "collect",widths = c(29.4, 3.7, 1)) & theme(legend.position = 'bottom')
* Save figure
plot<-gg1+theme(axis.text = element_text(size=6),
axis.title = element_text(size=7),
legend.text = element_text(size=7),
legend.title = element_text(size=8))+
gg2+theme(axis.text = element_text(size=6),
axis.title = element_text(size=7),
legend.text = element_text(size=7),
legend.title = element_text(size=8))+
gg3 +theme(axis.text = element_text(size=6),
axis.title = element_text(size=7),
legend.text = element_text(size=7),
legend.title = element_text(size=8))+
plot_layout(guides = "collect",widths = c(29.4, 3.7, 1)) & theme(legend.position = 'bottom')
ggsave('../results/croc_clusters_vs_repeats.pdf',plot, width = 5, height = 5)
ggplot(rep,aes(x=repeat_content))+geom_histogram()
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
library(GenomicRanges)
## Loading required package: stats4
## Loading required package: BiocGenerics
##
## Attaching package: 'BiocGenerics'
## The following object is masked from 'package:limma':
##
## plotMA
## The following objects are masked from 'package:lubridate':
##
## intersect, setdiff, union
## The following objects are masked from 'package:dplyr':
##
## combine, intersect, setdiff, union
## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, basename, cbind, colnames,
## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
## union, unique, unsplit, which.max, which.min
## Loading required package: S4Vectors
## Warning: package 'S4Vectors' was built under R version 4.1.3
##
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:gplots':
##
## space
## The following objects are masked from 'package:lubridate':
##
## second, second<-
## The following objects are masked from 'package:dplyr':
##
## first, rename
## The following object is masked from 'package:tidyr':
##
## expand
## The following objects are masked from 'package:base':
##
## expand.grid, I, unname
## Loading required package: IRanges
##
## Attaching package: 'IRanges'
## The following object is masked from 'package:lubridate':
##
## %within%
## The following objects are masked from 'package:dplyr':
##
## collapse, desc, slice
## The following object is masked from 'package:purrr':
##
## reduce
## Loading required package: GenomeInfoDb
croc_l<-read.delim2("../../03_transcriptomic_analysis/analysis_and_temp_files/08_dge_culture_lichen/croc_lichen_upregulated.txt",header=F)
croc_c<-read.delim2("../../03_transcriptomic_analysis/analysis_and_temp_files/08_dge_culture_lichen/croc_culture_upregulated.txt",header=F)
repeat_range <- GRanges(seqnames=rep$contig,ranges=IRanges(rep$window_start, rep$window_start+9999),repeat_content = rep$repeat_content)
croc_l_range <- GRanges(seqnames=croc_l$V1,ranges=IRanges(croc_l$V4, croc_l$V5),genes=croc_l$V9)
croc_c_range <- GRanges(seqnames=croc_c$V1,ranges=IRanges(croc_c$V4, croc_c$V5),genes=croc_c$V9)
repeat_croc_l <- repeat_range[countOverlaps(repeat_range, croc_l_range ) > 0]
repeat_croc_l2 <- repeat_croc_l[repeat_croc_l$repeat_content > 0.5]
croc_l_range[countOverlaps(croc_l_range,repeat_croc_l2) > 0]
## GRanges object with 8 ranges and 1 metadata column:
## seqnames ranges strand | genes
## <Rle> <IRanges> <Rle> | <character>
## [1] Xp_GTX0501_12 19342-42764 * | XANPAGTX0501_007271-..
## [2] Xp_GTX0501_14 137017-141122 * | XANPAGTX0501_008007-..
## [3] Xp_GTX0501_18 366441-424180 * | XANPAGTX0501_009046-..
## [4] Xp_GTX0501_2 399739-424931 * | XANPAGTX0501_001015-..
## [5] Xp_GTX0501_2 2298121-2324687 * | XANPAGTX0501_001710-..
## [6] Xp_GTX0501_21 183347-198083 * | XANPAGTX0501_009435-..
## [7] Xp_GTX0501_30 15022-50184 * | XANPAGTX0501_010180-..
## [8] Xp_GTX0501_8 1503462-1527344 * | XANPAGTX0501_005697-..
## -------
## seqinfo: 33 sequences from an unspecified genome; no seqlengths
library(GenomicRanges)
repeat_croc_c <- repeat_range[countOverlaps(repeat_range, croc_c_range ) > 0]
repeat_croc_c2 <- repeat_croc_l[repeat_croc_c$repeat_content > 0.5]
croc_c_range[countOverlaps(croc_c_range,repeat_croc_c2) > 0]
## GRanges object with 2 ranges and 1 metadata column:
## seqnames ranges strand | genes
## <Rle> <IRanges> <Rle> | <character>
## [1] Xp_GTX0501_13 711348-737772 * | XANPAGTX0501_007924-..
## [2] Xp_GTX0501_5 27829-113271 * | XANPAGTX0501_003202-..
## -------
## seqinfo: 26 sequences from an unspecified genome; no seqlengths